diff --git a/gitnexus/src/storage/storage-resolver.ts b/gitnexus/src/storage/storage-resolver.ts
index b44dcc4ad..1578b04c1 100644
--- a/gitnexus/src/storage/storage-resolver.ts
+++ b/gitnexus/src/storage/storage-resolver.ts
@@ -690,6 +690,20 @@ export const requireDeletableStoragePath = async (entry: {
 
   const expectedStoragePath = defaultStoragePath(repoPath);
   const storageIsLocal = isRepositoryLocalStoragePath(repoPath, actualStoragePath);
+  // Lookup may normalize extended-length paths, but deletion keeps the legacy
+  // fail-closed rule for a local registry entry with mixed namespace spellings.
+  if (
+    process.platform === 'win32' &&
+    storageIsLocal &&
+    expectedStoragePath.startsWith('\\\\?\\') !== actualStoragePath.startsWith('\\\\?\\')
+  ) {
+    throw new StorageDeletionError(
+      expectedStoragePath,
+      actualStoragePath,
+      undefined,
+      'repository-local storage must use the same extended-length path spelling as the repository',
+    );
+  }
   const comparableStorage = comparablePath(actualStoragePath);
   const comparableRepo = comparablePath(repoPath);
   const comparableRoot = comparablePath(path.parse(actualStoragePath).root);
diff --git a/gitnexus/test/unit/canonicalize-path-long-path-prefix.test.ts b/gitnexus/test/unit/canonicalize-path-long-path-prefix.test.ts
index 0e4730a00..35bf15915 100644
--- a/gitnexus/test/unit/canonicalize-path-long-path-prefix.test.ts
+++ b/gitnexus/test/unit/canonicalize-path-long-path-prefix.test.ts
@@ -74,6 +74,7 @@ import {
   type RegistryEntry,
 } from '../../src/storage/repo-manager.js';
 import { resolveRegisteredRepoEntry } from '../../src/server/api.js';
+import { requireDeletableStoragePath } from '../../src/storage/storage-resolver.js';
 
 /**
  * The lookup every registry consumer performs — `resolveRegistryEntry`,
@@ -164,6 +165,19 @@ describe('assertSafeStoragePath vs the `\\\\?\\` prefix (#2667)', () => {
       assertSafeStoragePath({ ...base, storagePath: 'D:\\Projects\\repo\\.gitnexus' }),
     ).rejects.toThrow();
   });
+
+  itOnWindows.each([
+    ['D:\\Projects\\repo', '\\\\?\\D:\\Projects\\repo\\.gitnexus'],
+    ['\\\\server\\share\\repo', '\\\\?\\UNC\\server\\share\\repo\\.gitnexus'],
+    ['\\\\?\\UNC\\server\\share\\repo', '\\\\server\\share\\repo\\.gitnexus'],
+  ])(
+    'rejects mixed namespace spellings in the shared deletion guard: %s',
+    async (repoPath, storagePath) => {
+      await expect(requireDeletableStoragePath({ path: repoPath, storagePath })).rejects.toThrow(
+        'same extended-length path spelling',
+      );
+    },
+  );
 });
 
 // The consumer surface the fix exists for: an MCP `repo` argument or an
diff --git a/gitnexus/test/unit/run-analyze-fts-repair.test.ts b/gitnexus/test/unit/run-analyze-fts-repair.test.ts
index 875e7dc47..8d68c8ddd 100644
--- a/gitnexus/test/unit/run-analyze-fts-repair.test.ts
+++ b/gitnexus/test/unit/run-analyze-fts-repair.test.ts
@@ -1909,6 +1909,7 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
   });
 
   it('preserves lastCommit / fileHashes / the dirty flag, and never restates a stale count', async () => {
+    vi.stubEnv('GITNEXUS_ATOMIC_WINDOWS_SWAP', '0');
     const STALE_COMMIT = '1111111111111111111111111111111111111111';
     const STALE_HASHES = { 'src/app.ts': 'stale-hash' };
     const LIVE_EMBEDDING_COUNT = 42;
@@ -2000,6 +2001,7 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
           _existingEmbeddings: unknown,
           pipelineOptions: EmbeddingPipelineOptions,
         ): Promise<EmbeddingPipelineResult> => {
+          snapshots.beforeCheckpoint = await loadMeta(storagePath);
           // Window 1 — fires before ANY embedding row exists.
           await pipelineOptions.onCheckpointWindowStart?.({
             nodesProcessed: 0,
@@ -2047,6 +2049,21 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
 
       expect(runEmbeddingPipeline).toHaveBeenCalledTimes(1);
 
+      // Windows writes in place and advances the dirty marker to FTS; a
+      // staged rebuild retains full-rebuild until publication. Neither marker
+      // may be changed or cleared by an embedding checkpoint.
+      const dirtyBeforeCheckpoint = snapshots.beforeCheckpoint?.incrementalInProgress;
+      expect(dirtyBeforeCheckpoint).toMatchObject({
+        phase: process.platform === 'win32' ? 'fts' : 'full-rebuild',
+      });
+      for (const snapshot of [
+        snapshots.windowStart,
+        snapshots.postWindow,
+        snapshots.secondWindow,
+      ]) {
+        expect(snapshot?.incrementalInProgress).toEqual(dirtyBeforeCheckpoint);
+      }
+
       // ── Window 1: the checkpoint landed… ──────────────────────────────
       expect(snapshots.windowStart).toMatchObject({
         embeddingCheckpoint: {
@@ -2063,7 +2080,7 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
       expect(snapshots.windowStart).toMatchObject({
         lastCommit: STALE_COMMIT,
         fileHashes: STALE_HASHES,
-        incrementalInProgress: { phase: 'full-rebuild' },
+        incrementalInProgress: dirtyBeforeCheckpoint,
         stats: { embeddings: 7 },
       });
       expect(snapshots.windowStart?.lastCommit).not.toBe(currentCommit);
@@ -2072,7 +2089,7 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
       expect(snapshots.postWindow).toMatchObject({
         lastCommit: STALE_COMMIT,
         fileHashes: STALE_HASHES,
-        incrementalInProgress: { phase: 'full-rebuild' },
+        incrementalInProgress: dirtyBeforeCheckpoint,
         stats: { embeddings: LIVE_EMBEDDING_COUNT },
       });