diff --git a/CHANGELOG.md b/CHANGELOG.md
index 75535a0bbd..1b28013cbd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -162,6 +162,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 #### MCP / indexing
 
+- File watching no longer drops the full re-scan a removed directory asks for when that sync fails, so the deleted files leave the index instead of lingering. (#1964)
 - Daemon startup and cleanup now preserve live legacy PID-only locks while still reclaiming dead or identity-disproved records, preventing two writers from serving the same project.
 - Incremental sync now keeps edge rebinding crash-safe: replacing a resolved edge with its recovery reference commits atomically, so an interruption cannot permanently remove the relationship.
 - Status now detects committed but unindexed changes and restored edits without scanning every source file; thanks @inth3shadows. (#1829)
diff --git a/__tests__/watcher.test.ts b/__tests__/watcher.test.ts
index 6b87a55ca9..a457468b92 100644
--- a/__tests__/watcher.test.ts
+++ b/__tests__/watcher.test.ts
@@ -968,6 +968,78 @@ describe('FileWatcher', () => {
       expect(calls[0]).toBeUndefined();
     });
 
+    it.each([
+      ['lock contention', () => new LockUnavailableError()],
+      ['sync failure', () => new Error('injected sync failure')],
+    ])('retries a full-only directory removal after %s (#1964)', async (_case, failure) => {
+      const syncFn = vi.fn()
+        .mockRejectedValueOnce(failure())
+        .mockResolvedValue({ filesChanged: 0, durationMs: 5 });
+      const watcher = newWatcher(syncFn, { debounceMs: 25 });
+      watcher.start();
+      try {
+        await watcher.waitUntilReady();
+        __emitWatchEventForTests(testDir, 'src/removed-dir');
+        await waitFor(() => syncFn.mock.calls.length >= 2, 4000);
+        expect(syncFn.mock.calls.map(call => call[0])).toEqual([undefined, undefined]);
+      } finally {
+        watcher.stop();
+      }
+    });
+
+    it('follows a scoped sync with a full scan when a directory is removed mid-sync (#1964)', async () => {
+      let release!: () => void;
+      const firstRun = new Promise<void>(resolve => { release = resolve; });
+      const calls: (string[] | undefined)[] = [];
+      const syncFn: SyncFn = async paths => {
+        calls.push(paths);
+        if (calls.length === 1) await firstRun;
+        return { filesChanged: 0, durationMs: 5 };
+      };
+      const watcher = newWatcher(syncFn, { debounceMs: 25 });
+      watcher.start();
+      try {
+        await watcher.waitUntilReady();
+        fs.writeFileSync(path.join(testDir, 'src', 'a.ts'), 'export const a = 1;');
+        __emitWatchEventForTests(testDir, 'src/a.ts');
+        await waitFor(() => calls.length === 1, 4000);
+        __emitWatchEventForTests(testDir, 'src/removed-dir');
+        release();
+        await waitFor(() => calls.length >= 2, 4000);
+        expect(calls).toEqual([['src/a.ts'], undefined]);
+      } finally {
+        release();
+        watcher.stop();
+      }
+    });
+
+    it('follows a scoped sync with a full scan when scope changes mid-sync (#1964)', async () => {
+      let release!: () => void;
+      const firstRun = new Promise<void>(resolve => { release = resolve; });
+      const calls: (string[] | undefined)[] = [];
+      const syncFn: SyncFn = async paths => {
+        calls.push(paths);
+        if (calls.length === 1) await firstRun;
+        return { filesChanged: 0, durationMs: 5 };
+      };
+      const watcher = newWatcher(syncFn, { debounceMs: 25 });
+      watcher.start();
+      try {
+        await watcher.waitUntilReady();
+        fs.writeFileSync(path.join(testDir, 'src', 'a.ts'), 'export const a = 1;');
+        __emitWatchEventForTests(testDir, 'src/a.ts');
+        await waitFor(() => calls.length === 1, 4000);
+        fs.writeFileSync(path.join(testDir, '.gitignore'), 'src/ignored/\n');
+        __emitWatchEventForTests(testDir, '.gitignore');
+        release();
+        await waitFor(() => calls.length >= 2, 4000);
+        expect(calls).toEqual([['src/a.ts'], undefined]);
+      } finally {
+        release();
+        watcher.stop();
+      }
+    });
+
     it('a lone file event fires on the quick window, well before the full debounce', async () => {
       const calls: (string[] | undefined)[] = [];
       const syncFn: SyncFn = async (paths?: string[]) => {
diff --git a/src/sync/watcher.ts b/src/sync/watcher.ts
index 5ea6436b6c..920a8a69c2 100644
--- a/src/sync/watcher.ts
+++ b/src/sync/watcher.ts
@@ -986,8 +986,10 @@ export class FileWatcher {
       // sync resets both counters so normal edits keep the fast debounce. Use
       // the larger streak so interleaved failures still back off. A degrade()
       // above already set `stopped`, so this won't reschedule a watcher that
-      // has given up.
-      if (this.pendingFiles.size > 0 && !this.stopped) {
+      // has given up. A directory removal whose full sync failed adds no
+      // pending file, only `needsFullScan` — it still owes the full reconcile
+      // it asked for (#1964).
+      if ((this.pendingFiles.size > 0 || this.needsFullScan) && !this.stopped) {
         const retryCount = Math.max(this.lockRetryCount, this.syncFailureRetryCount);
         if (retryCount > 0) {
           const retryDelayMs = Math.min(