diff --git a/gitnexus/src/core/run-analyze.ts b/gitnexus/src/core/run-analyze.ts
index d18185824..c7c945afb 100644
--- a/gitnexus/src/core/run-analyze.ts
+++ b/gitnexus/src/core/run-analyze.ts
@@ -669,6 +669,7 @@ export async function runFullAnalysis(
 
     // ── Phase 3: FTS (85–90%) ─────────────────────────────────────────
     progress('fts', 85, 'Creating search indexes...');
+    let ftsIndexed = false;
     try {
       await createSearchFTSIndexes({
         onIndexStart: options.verbose
@@ -684,11 +685,17 @@ export async function runFullAnalysis(
           `⚠️ FTS verification warning - missing indexes: ${missingIndexNames.join(', ')}. ` +
             'BM25 keyword search will be degraded. Upgrade macOS or run on a compatible platform to enable FTS.',
         );
+        progress('fts', 90, 'Search indexes degraded (BM25 unavailable)');
       } else {
+        ftsIndexed = true;
         progress('fts', 90, 'Search indexes ready');
       }
     } catch (ftsErr: unknown) {
       const ftsMsg = ftsErr instanceof Error ? ftsErr.message : String(ftsErr);
+      // Only suppress known FTS-extension-unavailable errors; rethrow DB/schema/programming errors.
+      if (!ftsMsg.includes('FTS extension unavailable')) {
+        throw ftsErr;
+      }
       log(`⚠️ FTS creation skipped (non-fatal): ${ftsMsg}`);
       progress('fts', 90, 'Search indexes skipped (FTS unavailable)');
     }
@@ -880,7 +887,7 @@ export async function runFullAnalysis(
       },
       capabilities: {
         graph: { provider: 'ladybugdb', status: runtimeCapabilities.graph },
-        fts: { provider: 'ladybugdb-fts', status: runtimeCapabilities.fts },
+        fts: { provider: 'ladybugdb-fts', status: ftsIndexed ? runtimeCapabilities.fts : 'degraded' },
         vectorSearch: {
           provider: effectiveSemanticMode === 'vector-index' ? 'ladybugdb-vector' : 'exact-scan',
           status: embeddingCount > 0 ? effectiveSemanticMode : 'unavailable',
diff --git a/gitnexus/test/unit/run-analyze-fts-repair.test.ts b/gitnexus/test/unit/run-analyze-fts-repair.test.ts
index 7b7030ee4..b755a8c2b 100644
--- a/gitnexus/test/unit/run-analyze-fts-repair.test.ts
+++ b/gitnexus/test/unit/run-analyze-fts-repair.test.ts
@@ -227,17 +227,33 @@ describe('runFullAnalysis FTS repair and verification failure paths', () => {
     const tmpRepo = await createTempDir('gitnexus-run-analyze-full-verify-fail-');
     try {
       const { runFullAnalysis } = await import('../../src/core/run-analyze.js');
+
+      const logMessages: string[] = [];
+      const progressMessages: string[] = [];
+
       // FTS verification failure is now non-fatal — analyze completes with a warning
       // instead of throwing, so embedding generation can proceed.
       const result = await runFullAnalysis(
         tmpRepo.dbPath,
         { force: true },
         {
-          onProgress: () => {},
+          onProgress: (_phase, _pct, msg) => {
+            if (msg) progressMessages.push(msg);
+          },
+          onLog: (msg: string) => {
+            logMessages.push(msg);
+          },
         },
       );
       expect(result).toBeDefined();
       expect(result.repoPath).toContain('gitnexus-run-analyze-full-verify-fail-');
+
+      // Verify warning was logged about missing FTS indexes
+      expect(logMessages.some((m) => /FTS verification warning/i.test(m))).toBe(true);
+
+      // Verify progress did NOT report "Search indexes ready" (it should report degraded)
+      expect(progressMessages).not.toContain('Search indexes ready');
+      expect(progressMessages.some((m) => /degraded|unavailable/i.test(m))).toBe(true);
     } finally {
       await tmpRepo.cleanup();
     }