diff --git a/gitnexus/src/core/lbug/lbug-adapter.ts b/gitnexus/src/core/lbug/lbug-adapter.ts
index 59f903261..92adff18a 100644
--- a/gitnexus/src/core/lbug/lbug-adapter.ts
+++ b/gitnexus/src/core/lbug/lbug-adapter.ts
@@ -4044,6 +4044,7 @@ export const buildFtsQueryCypher = (
  * @param query - Search query string
  * @param limit - Maximum results
  * @param conjunctive - If true, all terms must match (AND); if false, any term matches (OR)
+ * @param missingIndex - Preserve the empty-result default, or propagate missing indexes for diagnostics
  * @returns Array of { node properties, score }
  */
 export const queryFTS = async (
@@ -4052,6 +4053,7 @@ export const queryFTS = async (
   query: string,
   limit: number = 20,
   conjunctive: boolean = false,
+  missingIndex: 'empty' | 'throw' = 'empty',
 ): Promise<
   Array<{ nodeId: string; name: string; filePath: string; score: number; [key: string]: any }>
 > => {
@@ -4082,7 +4084,7 @@ export const queryFTS = async (
     // NEW-6 — this used to be a bare `.includes('does not exist')` check
     // that could not tell the two apart).
     const message = e instanceof Error ? e.message : String(e);
-    if (classifyFtsQueryError(message) === 'missing-index') {
+    if (missingIndex === 'empty' && classifyFtsQueryError(message) === 'missing-index') {
       return [];
     }
     throw e;
diff --git a/gitnexus/src/core/search/bm25-index.ts b/gitnexus/src/core/search/bm25-index.ts
index 8aaa279ef..c105a62a3 100644
--- a/gitnexus/src/core/search/bm25-index.ts
+++ b/gitnexus/src/core/search/bm25-index.ts
@@ -47,6 +47,8 @@ export interface FTSSearchResponse {
    * which only does so when every table failed).
    */
   nonBenignErrors?: string[];
+  /** Configured table.index names that could not be queried because their index is missing. */
+  missingIndexes?: string[];
 }
 
 /**
@@ -142,6 +144,7 @@ export const searchFTSFromLbug = async (
   const resultsByIndex: any[][] = [];
   let queriesSucceeded = 0;
   const nonBenignErrors: string[] = [];
+  const missingIndexes: string[] = [];
 
   const ftsExtension = getExtensionCapabilities().find((c) => c.name === 'fts');
   if (ftsExtension && !ftsExtension.loaded) {
@@ -171,24 +174,28 @@ export const searchFTSFromLbug = async (
       if (outcome.rows) {
         queriesSucceeded++;
         resultsByIndex.push(outcome.rows);
-      } else if (!outcome.benign) {
+      } else if (outcome.benign) {
+        missingIndexes.push(`${table}.${indexName}`);
+      } else {
         nonBenignErrors.push(redactPaths(outcome.message ?? 'Unknown FTS query error'));
       }
     }
   } else {
     // Use core lbug adapter (CLI / pipeline context) — also sequential for safety.
-    // tri-review Residual-1: `queryFTS` itself only swallows a genuinely-missing
-    // index (via the SAME classifyFtsQueryError this module re-exports); a
-    // missing-table or real query error rethrows here — track it the same way
-    // the MCP pool path does instead of a bare `catch {}` that dropped it.
+    // Opt into missing-index propagation so absent indexes cannot masquerade
+    // as successful zero-match queries. Keep core/pool classification identical.
     for (const { table, indexName } of FTS_INDEXES) {
       try {
-        const result = await queryFTS(table, indexName, searchQuery, limit, false);
+        const result = await queryFTS(table, indexName, searchQuery, limit, false, 'throw');
         queriesSucceeded++;
         resultsByIndex.push(result);
       } catch (e) {
         const message = e instanceof Error ? e.message : String(e);
-        nonBenignErrors.push(redactPaths(message));
+        if (classifyFtsQueryError(message) === 'missing-index') {
+          missingIndexes.push(`${table}.${indexName}`);
+        } else {
+          nonBenignErrors.push(redactPaths(message));
+        }
       }
     }
   }
@@ -234,5 +241,6 @@ export const searchFTSFromLbug = async (
     })),
     ftsAvailable,
     ...(nonBenignErrors.length > 0 && { nonBenignErrors }),
+    ...(missingIndexes.length > 0 && { missingIndexes }),
   };
 };
diff --git a/gitnexus/src/core/search/fts-indexes.ts b/gitnexus/src/core/search/fts-indexes.ts
index 2070fadf3..5f8b59f13 100644
--- a/gitnexus/src/core/search/fts-indexes.ts
+++ b/gitnexus/src/core/search/fts-indexes.ts
@@ -110,19 +110,21 @@ export const ftsDegradedWarning = (
 };
 
 /**
- * Warning for when the FTS extension is loaded and indexes exist, but every
- * configured table's query failed for a real, non-benign reason (timeout,
- * connection reset, native fault) — as opposed to `ftsDegradedWarning`'s
- * missing-index case. `--repair-fts` will not fix a query/connection error,
- * so this deliberately does NOT suggest it: reusing the missing-index
- * message here would reproduce, for this cause, the exact misleading
- * "run --repair-fts" guidance #2767 itself was about (tri-review NEW-1).
+ * Warning when no FTS query succeeded and at least one failed for a real,
+ * non-benign reason (timeout, connection reset, native fault). `--repair-fts`
+ * will not fix those errors. If indexes are also missing, the caller composes
+ * their repair guidance separately; do not deny that additional failure cause.
  */
-export const ftsQueryFailedWarning = (context: FtsWarningContext): string =>
+export const ftsQueryFailedWarning = (
+  context: FtsWarningContext,
+  hasMissingIndexes = false,
+): string =>
   'FTS keyword search failed — every configured index query returned an error' +
   (context.lastErrorRedacted ? ` (${context.lastErrorRedacted})` : '') +
-  '; results do not include keyword matches. This is not a missing-index ' +
-  'condition — see server logs for details.' +
+  '; results do not include keyword matches. ' +
+  (hasMissingIndexes
+    ? 'See server logs for query error details.'
+    : 'This is not a missing-index condition — see server logs for details.') +
   ` (resolved: ${formatResolvedSuffix(context)})`;
 
 // Stemmers shipped by the LadybugDB FTS extension. Mirrors the lowercase token
diff --git a/gitnexus/src/mcp/local/local-backend.ts b/gitnexus/src/mcp/local/local-backend.ts
index 5b2f62a9c..cb8546543 100644
--- a/gitnexus/src/mcp/local/local-backend.ts
+++ b/gitnexus/src/mcp/local/local-backend.ts
@@ -3172,6 +3172,7 @@ export class LocalBackend {
     // regardless of whether OTHER tables succeeded — previously a real error
     // on N-1 of N tables while one succeeded left zero diagnostic trail.
     const ftsQueryErrors = bm25SearchResult?.nonBenignErrors;
+    const ftsMissingIndexes = bm25SearchResult?.missingIndexes;
     if (ftsQueryErrors) {
       // tri-review NEW-5: these strings are already classified non-benign by
       // classifyFtsQueryError — do NOT route them through logQueryError,
@@ -3661,13 +3662,15 @@ export class LocalBackend {
         branch: repo.branch,
         indexedAt: this.lastObservedPoolState.get(repo.lbugPath)?.indexedAt ?? repo.indexedAt,
       };
-      // tri-review NEW-1: every table failing for a REAL error (timeout,
-      // connection reset) is not a missing-index condition — `ftsDegradedWarning`'s
-      // "run --repair-fts" headline won't fix it. Route to a dedicated message
-      // instead of burying the real cause as a trailing suffix on bad advice.
+      // Real errors (timeout, connection reset) need their own diagnosis.
+      // When some indexes are also missing, preserve both causes and append
+      // their repair guidance below even though no FTS query succeeded.
       warnings.push(
         ftsQueryErrors
-          ? ftsQueryFailedWarning({ ...warningContext, lastErrorRedacted: ftsQueryErrors[0] })
+          ? ftsQueryFailedWarning(
+              { ...warningContext, lastErrorRedacted: ftsQueryErrors[0] },
+              !!ftsMissingIndexes?.length,
+            )
           : ftsDegradedWarning(warningContext, ftsDisabledReason),
       );
     } else if (ftsQueryErrors) {
@@ -3680,6 +3683,12 @@ export class LocalBackend {
         `FTS keyword search partially failed — ${ftsQueryErrors.length} of the configured indexes hit a query error and were skipped; results may be missing matches from those node types (see server logs).`,
       );
     }
+    if (ftsMissingIndexes?.length && (ftsUsed || ftsQueryErrors)) {
+      warnings.push(
+        `FTS keyword search is incomplete: missing configured indexes (${ftsMissingIndexes.join(', ')}). ` +
+          'Results may be missing matches from those node types. Run `gitnexus analyze --repair-fts`.',
+      );
+    }
     // #2331: a CJK query against a server process resolving
     // GITNEXUS_FTS_CJK_SEGMENTATION to 'none' silently misses sub-phrase
     // matches with no other signal — this is the only place an agent driving
@@ -3811,7 +3820,7 @@ export class LocalBackend {
     // #2767: a partial FTS failure (some tables ok, one or more real errors)
     // is as much a "results may be incomplete" signal as enrichmentDegraded —
     // flag it the same way rather than only via the warning string.
-    const ftsPartial = ftsUsed && !!ftsQueryErrors;
+    const ftsPartial = ftsUsed && (!!ftsQueryErrors || !!ftsMissingIndexes?.length);
 
     return {
       processes,
@@ -3832,7 +3841,12 @@ export class LocalBackend {
     query: string,
     limit: number,
     disabledReason?: FtsDisabledReason,
-  ): Promise<{ results: any[]; ftsUsed: boolean; nonBenignErrors?: string[] }> {
+  ): Promise<{
+    results: any[];
+    ftsUsed: boolean;
+    nonBenignErrors?: string[];
+    missingIndexes?: string[];
+  }> {
     if (disabledReason) return { results: [], ftsUsed: false };
     let searchFTSFromLbug;
     try {
@@ -3866,6 +3880,7 @@ export class LocalBackend {
     const bm25Results = ftsResponse?.results ?? [];
     const ftsUsed = ftsResponse?.ftsAvailable ?? false;
     const nonBenignErrors = ftsResponse?.nonBenignErrors;
+    const missingIndexes = ftsResponse?.missingIndexes;
 
     const results: any[] = [];
 
@@ -3939,7 +3954,12 @@ export class LocalBackend {
       }
     }
 
-    return { results, ftsUsed, ...(nonBenignErrors && { nonBenignErrors }) };
+    return {
+      results,
+      ftsUsed,
+      ...(nonBenignErrors && { nonBenignErrors }),
+      ...(missingIndexes && { missingIndexes }),
+    };
   }
 
   /**
diff --git a/gitnexus/test/fixtures/local-backend-seed.ts b/gitnexus/test/fixtures/local-backend-seed.ts
index 4878348b2..1f7fd02c9 100644
--- a/gitnexus/test/fixtures/local-backend-seed.ts
+++ b/gitnexus/test/fixtures/local-backend-seed.ts
@@ -1,4 +1,5 @@
 import type { FTSIndexDef } from '../helpers/test-indexed-db.js';
+import { FTS_INDEXES } from '../../src/core/search/fts-schema.js';
 
 export const LOCAL_BACKEND_SEED_DATA = [
   // Files
@@ -60,9 +61,8 @@ export const LOCAL_BACKEND_SEED_DATA = [
    CREATE (c)-[:CodeRelation {type: 'HAS_METHOD', confidence: 1.0, reason: 'class-method', step: 0}]->(m)`,
 ];
 
-export const LOCAL_BACKEND_FTS_INDEXES: FTSIndexDef[] = [
-  { table: 'Function', indexName: 'function_fts', columns: ['name', 'content', 'description'] },
-  { table: 'Class', indexName: 'class_fts', columns: ['name', 'content', 'description'] },
-  { table: 'Method', indexName: 'method_fts', columns: ['name', 'content', 'description'] },
-  { table: 'File', indexName: 'file_fts', columns: ['name', 'content'] },
-];
+// Healthy-backend fixtures must mirror the complete configured search index set.
+// The old four-table subset is now correctly reported as partial FTS coverage.
+export const LOCAL_BACKEND_FTS_INDEXES: FTSIndexDef[] = FTS_INDEXES.map(
+  ({ table, indexName, properties }) => ({ table, indexName, columns: [...properties] }),
+);
diff --git a/gitnexus/test/integration/fts-repair-warm-session.test.ts b/gitnexus/test/integration/fts-repair-warm-session.test.ts
index 2550ba874..ac9ce2713 100644
--- a/gitnexus/test/integration/fts-repair-warm-session.test.ts
+++ b/gitnexus/test/integration/fts-repair-warm-session.test.ts
@@ -32,6 +32,7 @@ const REQUIRE_FTS = process.env.GITNEXUS_REQUIRE_FTS === '1';
 type QueryResult = {
   error?: unknown;
   warning?: string;
+  partial?: boolean;
   definitions?: Array<{ id: string }>;
   process_symbols?: Array<{ id: string }>;
 };
@@ -40,7 +41,8 @@ const matchedIds = (r: QueryResult): string[] =>
   [...(r.process_symbols ?? []), ...(r.definitions ?? [])].map((s) => s.id);
 
 const ftsMissing = (r: QueryResult): boolean =>
-  typeof r.warning === 'string' && /FTS indexes missing/i.test(r.warning);
+  typeof r.warning === 'string' &&
+  /FTS indexes missing|missing configured indexes/i.test(r.warning);
 
 /**
  * Poll the SAME warm `LocalBackend` until it stops reporting FTS-missing, or
@@ -90,14 +92,14 @@ describe('warm MCP session observes an in-place --repair-fts rebuild (#2767)', (
     await tmpHandle.cleanup();
   });
 
-  it(
-    'a warm session transitions from FTS-unavailable to FTS-available without restarting, after an out-of-band --repair-fts',
+  it.each(['all', 'Function'] as const)(
+    'a warm session repairs missing %s indexes without restarting',
     { timeout: 60_000 },
-    async (ctx) => {
+    async (missing, ctx) => {
       const adapter = await import('../../src/core/lbug/lbug-adapter.js');
       const { createSearchFTSIndexes } = await import('../../src/core/search/fts-indexes.js');
 
-      // ── Step 1: build the index WITHOUT FTS (analyzed before repair) ────
+      // ── Step 1: build an index with all or just one FTS index missing ──
       await adapter.initLbug(lbugPath);
 
       const ftsAvailable = await adapter.loadFTSExtension(undefined, {
@@ -118,6 +120,10 @@ describe('warm MCP session observes an in-place --repair-fts rebuild (#2767)', (
       await adapter.executeQuery(
         `CREATE (n:Function {id: 'func:login', name: 'login', filePath: 'src/auth.ts', startLine: 1, endLine: 3, content: 'function login() { return true; }'})`,
       );
+      if (missing === 'Function') {
+        await createSearchFTSIndexes();
+        await adapter.dropFTSIndex('Function', 'function_fts');
+      }
       await adapter.flushWAL();
       await adapter.closeLbug();
 
@@ -129,7 +135,10 @@ describe('warm MCP session observes an in-place --repair-fts rebuild (#2767)', (
         stats: { files: 1, nodes: 1 },
         capabilities: {
           graph: { provider: 'ladybugdb', status: 'available' },
-          fts: { provider: 'ladybugdb-fts', status: 'unavailable' },
+          fts: {
+            provider: 'ladybugdb-fts',
+            status: missing === 'all' ? 'unavailable' : 'available',
+          },
           vectorSearch: { provider: 'exact-scan', status: 'unavailable', exactScanLimit: 0 },
         },
       };
@@ -142,6 +151,10 @@ describe('warm MCP session observes an in-place --repair-fts rebuild (#2767)', (
       const before = await backend.callTool('query', { query: 'login' });
       expect(before.error).toBeUndefined();
       expect(ftsMissing(before)).toBe(true);
+      if (missing === 'Function') {
+        expect(before.partial).toBe(true);
+        expect(before.warning).toContain('Function.function_fts');
+      }
 
       // ── Step 3: out-of-band --repair-fts (separate writable session) ────
       // Same production functions the repair-fts branch of runFullAnalysis
@@ -163,6 +176,7 @@ describe('warm MCP session observes an in-place --repair-fts rebuild (#2767)', (
       const after = await waitForFtsRecognized(backend, 'login');
       expect(after.error).toBeUndefined();
       expect(ftsMissing(after)).toBe(false);
+      expect(after.partial).toBeUndefined();
       expect(matchedIds(after)).toContain('func:login');
     },
   );
diff --git a/gitnexus/test/unit/bm25-search.test.ts b/gitnexus/test/unit/bm25-search.test.ts
index 793cf7aae..08b2fc46a 100644
--- a/gitnexus/test/unit/bm25-search.test.ts
+++ b/gitnexus/test/unit/bm25-search.test.ts
@@ -647,3 +647,125 @@ describe('BM25 search', () => {
     });
   });
 });
+
+describe('FTS index completeness', () => {
+  beforeEach(async () => {
+    resetExtensionState();
+    mockExecuteParameterized.mockReset();
+    const { queryFTS } = await import('../../src/core/lbug/lbug-adapter.js');
+    vi.mocked(queryFTS).mockReset();
+  });
+
+  const missing = (table: string, indexName: string) =>
+    new Error(`Binder exception: Table ${table} doesn't have an index with name ${indexName}.`);
+
+  for (const pooled of [false, true]) {
+    const mode = pooled ? 'pool' : 'core';
+    const repo = pooled ? 'completeness-test' : undefined;
+
+    async function useOutcome(outcome: (table: string, indexName: string) => Promise<any[]>) {
+      const { queryFTS } = await import('../../src/core/lbug/lbug-adapter.js');
+      vi.mocked(queryFTS).mockImplementation((table, indexName) => outcome(table, indexName));
+      mockExecuteParameterized.mockImplementation(async (_repo: string, cypher: string) => {
+        const match = cypher.match(/QUERY_FTS_INDEX\('([^']+)', '([^']+)'/);
+        return outcome(match![1], match![2]);
+      });
+    }
+
+    it(`${mode}: distinguishes healthy zero matches from missing indexes`, async () => {
+      await useOutcome(async () => []);
+      const result = await searchFTSFromLbug('no matches', 5, repo);
+      expect(result).toEqual({ results: [], ftsAvailable: true });
+    });
+
+    it(`${mode}: reports one missing index while retaining successful matches`, async () => {
+      await useOutcome(async (table, indexName) => {
+        if (table === 'Function') throw missing(table, indexName);
+        if (table !== 'File') return [];
+        return pooled
+          ? [{ node: { filePath: 'src/auth.ts', id: 'file:auth' }, score: 3 }]
+          : [{ filePath: 'src/auth.ts', nodeId: 'file:auth', score: 3 }];
+      });
+      const result = await searchFTSFromLbug('auth', 5, repo);
+      expect(result.ftsAvailable).toBe(true);
+      expect(result.results[0]).toMatchObject({ filePath: 'src/auth.ts', score: 3 });
+      expect(result.missingIndexes).toEqual(['Function.function_fts']);
+      expect(result.nonBenignErrors).toBeUndefined();
+    });
+
+    it(`${mode}: reports all missing indexes without claiming FTS is available`, async () => {
+      await useOutcome(async (table, indexName) => {
+        throw missing(table, indexName);
+      });
+      const result = await searchFTSFromLbug('auth', 5, repo);
+      expect(result.ftsAvailable).toBe(false);
+      expect(result.results).toEqual([]);
+      if (!pooled) {
+        const { queryFTS } = await import('../../src/core/lbug/lbug-adapter.js');
+        for (const { table, indexName } of FTS_INDEXES) {
+          expect(queryFTS).toHaveBeenCalledWith(table, indexName, 'auth', 5, false, 'throw');
+        }
+      }
+      expect(result.missingIndexes).toEqual(
+        FTS_INDEXES.map(({ table, indexName }) => `${table}.${indexName}`),
+      );
+      expect(result.nonBenignErrors).toBeUndefined();
+    });
+
+    it(`${mode}: preserves redacted real errors alongside missing-index diagnostics`, async () => {
+      await useOutcome(async (table, indexName) => {
+        if (table === 'Function') throw missing(table, indexName);
+        if (table === 'Class')
+          throw new Error('connection reset at /home/alice/private/index.lbug');
+        return [];
+      });
+      const result = await searchFTSFromLbug('auth', 5, repo);
+      expect(result.ftsAvailable).toBe(true);
+      expect(result.missingIndexes).toEqual(['Function.function_fts']);
+      expect(result.nonBenignErrors).toHaveLength(1);
+      expect(result.nonBenignErrors![0]).toContain('connection reset');
+      expect(JSON.stringify(result)).not.toContain('/home/alice');
+    });
+
+    it(`${mode}: retains both failure causes when no configured index query succeeds`, async () => {
+      await useOutcome(async (table, indexName) => {
+        if (table === 'Function') throw missing(table, indexName);
+        throw new Error('connection reset at /home/alice/private/index.lbug');
+      });
+
+      const result = await searchFTSFromLbug('auth', 5, repo);
+
+      expect(result.ftsAvailable).toBe(false);
+      expect(result.results).toEqual([]);
+      expect(result.missingIndexes).toEqual(['Function.function_fts']);
+      expect(result.nonBenignErrors).toEqual(
+        Array(FTS_INDEXES.length - 1).fill('connection reset at <path>'),
+      );
+    });
+
+    it(`${mode}: clears missing-index diagnostics after a repaired query`, async () => {
+      await useOutcome(async (table, indexName) => {
+        if (table === 'Function') throw missing(table, indexName);
+        return [];
+      });
+      expect((await searchFTSFromLbug('auth', 5, repo)).missingIndexes).toEqual([
+        'Function.function_fts',
+      ]);
+      await useOutcome(async () => []);
+      expect(await searchFTSFromLbug('auth', 5, repo)).toEqual({ results: [], ftsAvailable: true });
+    });
+
+    it(`${mode}: explicit opt-out makes no queries and emits no missing-index diagnosis`, async () => {
+      await useOutcome(async (table, indexName) => {
+        throw missing(table, indexName);
+      });
+      expect(await searchFTSFromLbug('auth', 5, repo, 'disabled-by-flag')).toEqual({
+        results: [],
+        ftsAvailable: false,
+      });
+      const { queryFTS } = await import('../../src/core/lbug/lbug-adapter.js');
+      expect(queryFTS).not.toHaveBeenCalled();
+      expect(mockExecuteParameterized).not.toHaveBeenCalled();
+    });
+  }
+});
diff --git a/gitnexus/test/unit/query-degraded-signal.test.ts b/gitnexus/test/unit/query-degraded-signal.test.ts
index a7ed807e8..f4c9e763c 100644
--- a/gitnexus/test/unit/query-degraded-signal.test.ts
+++ b/gitnexus/test/unit/query-degraded-signal.test.ts
@@ -42,6 +42,7 @@ vi.mock('../../src/storage/repo-manager.js', async (importOriginal) => {
 });
 
 import { LocalBackend } from '../../src/mcp/local/local-backend';
+import { resetExtensionState } from '../../src/core/lbug/extension-loader.js';
 
 // A backend whose hybrid search yields exactly one matched symbol, so the
 // enrichment chunk loop runs and can be made to fail. `ftsUsed` is parameterized
@@ -415,3 +416,100 @@ describe('query: degraded-enrichment signal', () => {
     }
   });
 });
+
+describe('query: partial missing FTS indexes', () => {
+  beforeEach(() => {
+    vi.clearAllMocks();
+    loadMetaMock.mockResolvedValue(null);
+    executeParameterizedMock.mockResolvedValue([]);
+  });
+  afterEach(() => vi.unstubAllEnvs());
+
+  it('returns successful symbols with a repair hint and partial flag when another index is missing', async () => {
+    const b = makeBackend(true) as any;
+    const resultWithMissing = await b.backend.bm25Search();
+    b.backend.bm25Search.mockResolvedValue({
+      ...resultWithMissing,
+      missingIndexes: ['Function.function_fts'],
+    });
+
+    const result = await runQuery(b);
+
+    expect(result.definitions.map((d: any) => d.id)).toContain('func:x');
+    expect(result.partial).toBe(true);
+    expect(result.warning).toContain('Function.function_fts');
+    expect(result.warning).toContain('repair-fts');
+  });
+
+  it('composes missing indexes with real FTS errors and enrichment failures', async () => {
+    const b = makeBackend(true, ['connection reset']) as any;
+    const resultWithMissing = await b.backend.bm25Search();
+    b.backend.bm25Search.mockResolvedValue({
+      ...resultWithMissing,
+      missingIndexes: ['Function.function_fts'],
+    });
+    executeParameterizedMock.mockImplementation(async (_repo: string, cypher: string) => {
+      if (cypher.includes('STEP_IN_PROCESS')) throw new Error('timed out');
+      return [];
+    });
+
+    const result = await runQuery(b);
+
+    expect(result.partial).toBe(true);
+    expect(result.warning).toContain('Function.function_fts');
+    expect(result.warning).toContain('FTS keyword search partially failed');
+    expect(result.warning).toContain('enrichment');
+  });
+});
+
+it('propagates missing-index diagnostics through the real bm25Search helper into query', async () => {
+  vi.clearAllMocks();
+  loadMetaMock.mockResolvedValue(null);
+  executeParameterizedMock.mockResolvedValue([]);
+  const search = await import('../../src/core/search/bm25-index.js');
+  const spy = vi.spyOn(search, 'searchFTSFromLbug').mockResolvedValue({
+    results: [],
+    ftsAvailable: true,
+    missingIndexes: ['Function.function_fts'],
+  });
+  try {
+    const b = makeBackend(true) as any;
+    b.backend.bm25Search = (LocalBackend.prototype as any).bm25Search;
+    const result = await runQuery(b);
+    expect(result.partial).toBe(true);
+    expect(result.warning).toContain('Function.function_fts');
+  } finally {
+    spy.mockRestore();
+  }
+});
+
+it('reports missing indexes and real errors when every FTS query fails through the search boundary', async () => {
+  vi.clearAllMocks();
+  resetExtensionState();
+  loadMetaMock.mockResolvedValue(null);
+  executeParameterizedMock.mockImplementation(async (_repo: string, cypher: string) => {
+    if (cypher.includes("QUERY_FTS_INDEX('Function'")) {
+      throw new Error(
+        "Binder exception: Table Function doesn't have an index with name function_fts.",
+      );
+    }
+    if (cypher.includes('QUERY_FTS_INDEX')) {
+      throw new Error('connection reset at /home/alice/private/index.lbug');
+    }
+    return [];
+  });
+  const b = makeBackend(false) as any;
+  b.backend.bm25Search = (LocalBackend.prototype as any).bm25Search;
+
+  const result = await runQuery(b);
+
+  expect(result.definitions).toEqual([]);
+  expect(result.warning).toContain('FTS keyword search failed');
+  expect(result.warning).toContain('connection reset at <path>');
+  expect(result.warning).toContain('Function.function_fts');
+  expect(result.warning).toContain('gitnexus analyze --repair-fts');
+  expect(result.warning).toContain('resolved: repo1');
+  expect(result.warning).not.toContain('not a missing-index');
+  expect(result.warning).not.toContain('partially failed');
+  expect(JSON.stringify(result)).not.toContain('/home/alice');
+});
diff --git a/gitnexus/test/unit/query-fts-missing-index.test.ts b/gitnexus/test/unit/query-fts-missing-index.test.ts
new file mode 100644
index 000000000..aa50a50bf
--- /dev/null
+++ b/gitnexus/test/unit/query-fts-missing-index.test.ts
@@ -0,0 +1,114 @@
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+import fs from 'node:fs/promises';
+import os from 'node:os';
+import path from 'node:path';
+
+const native = vi.hoisted(() => ({
+  error: undefined as string | undefined,
+  params: [] as unknown[],
+}));
+
+// Control the native statement result, while exercising the real adapter's
+// connection lock, prepared-query path and missing-index error handling.
+vi.mock('@ladybugdb/core', () => {
+  const emptyResult = {
+    getAll: async () => [],
+    close: async () => {},
+    isSuccess: () => true,
+    getErrorMessage: async () => '',
+  };
+  class Database {
+    async init() {}
+    async close() {}
+  }
+  class Connection {
+    async query() {
+      return emptyResult;
+    }
+    async prepare() {
+      return {
+        isSuccess: () => native.error === undefined,
+        getErrorMessage: async () => native.error ?? '',
+      };
+    }
+    async execute(_statement: unknown, params: unknown) {
+      native.params.push(params);
+      return emptyResult;
+    }
+    async close() {}
+  }
+  const mod = { Database, Connection };
+  return { ...mod, default: mod, lbug: mod };
+});
+
+import { closeLbug, queryFTS, withLbugDb } from '../../src/core/lbug/lbug-adapter.js';
+
+const MISSING = "Binder exception: Table Function doesn't have an index with name function_fts.";
+
+describe('queryFTS missing-index diagnostics', () => {
+  let dir: string;
+  let dbPath: string;
+  beforeEach(async () => {
+    native.error = undefined;
+    native.params = [];
+    dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gitnexus-test-'));
+    dbPath = path.join(dir, 'lbug');
+    await fs.writeFile(dbPath, '');
+  });
+  afterEach(async () => {
+    await closeLbug();
+    await fs.rm(dir, { recursive: true, force: true });
+  });
+
+  it('retains the existing empty-result default for a missing index', async () => {
+    await withLbugDb(
+      dbPath,
+      async () => {
+        native.error = MISSING;
+        expect(await queryFTS('Function', 'function_fts', 'auth')).toEqual([]);
+      },
+      { readOnly: true, skipFts: true },
+    );
+  });
+
+  it('can propagate a missing index so search does not count it as a successful zero-match query', async () => {
+    await withLbugDb(
+      dbPath,
+      async () => {
+        native.error = MISSING;
+        await expect(
+          queryFTS('Function', 'function_fts', 'auth', 5, false, 'throw'),
+        ).rejects.toThrow(MISSING);
+      },
+      { readOnly: true, skipFts: true },
+    );
+  });
+
+  it('preserves prepared query binding and successful empty results in diagnostic mode', async () => {
+    await withLbugDb(
+      dbPath,
+      async () => {
+        const query = "auth' DELETE n";
+        expect(await queryFTS('Function', 'function_fts', query, 5, false, 'throw')).toEqual([]);
+        expect(native.params).toEqual([{ query }]);
+      },
+      { readOnly: true, skipFts: true },
+    );
+  });
+
+  it('still propagates real failures in either missing-index mode', async () => {
+    await withLbugDb(
+      dbPath,
+      async () => {
+        native.error = 'Runtime exception: connection reset';
+        await expect(queryFTS('Function', 'function_fts', 'auth')).rejects.toThrow(
+          'connection reset',
+        );
+        await expect(
+          queryFTS('Function', 'function_fts', 'auth', 5, false, 'throw'),
+        ).rejects.toThrow('connection reset');
+      },
+      { readOnly: true, skipFts: true },
+    );
+  });
+});