diff --git a/src/resources/extensions/gsd/state.ts b/src/resources/extensions/gsd/state.ts
index dc37405f7..a3694c61d 100644
--- a/src/resources/extensions/gsd/state.ts
+++ b/src/resources/extensions/gsd/state.ts
@@ -48,6 +48,7 @@ import {
   getSliceTasks,
   getReplanHistory,
   getSlice,
+  insertMilestone,
   type MilestoneRow,
   type SliceRow,
   type TaskRow,
@@ -257,7 +258,24 @@ function isStatusDone(status: string): boolean {
 export async function deriveStateFromDb(basePath: string): Promise<GSDState> {
   const requirements = parseRequirementCounts(await loadFile(resolveGsdRootFile(basePath, "REQUIREMENTS")));
 
-  const allMilestones = getAllMilestones();
+  let allMilestones = getAllMilestones();
+
+  // Incremental disk→DB sync: milestone directories created outside the DB
+  // write path (via /gsd queue, manual mkdir, or complete-milestone writing the
+  // next CONTEXT.md) are never inserted by the initial migration guard in
+  // auto-start.ts because that guard only runs when gsd.db doesn't exist yet.
+  // Reconcile here so deriveStateFromDb never silently misses queued milestones.
+  // insertMilestone uses INSERT OR IGNORE, so this is safe to call every time.
+  const dbIdSet = new Set(allMilestones.map(m => m.id));
+  const diskIds = findMilestoneIds(basePath);
+  let synced = false;
+  for (const diskId of diskIds) {
+    if (!dbIdSet.has(diskId) && !isGhostMilestone(basePath, diskId)) {
+      insertMilestone({ id: diskId, status: 'active' });
+      synced = true;
+    }
+  }
+  if (synced) allMilestones = getAllMilestones();
 
   // Parallel worker isolation: when locked, filter to just the locked milestone
   const milestoneLock = process.env.GSD_MILESTONE_LOCK;
diff --git a/src/resources/extensions/gsd/tests/derive-state-db.test.ts b/src/resources/extensions/gsd/tests/derive-state-db.test.ts
index f50618f89..2b8d304fb 100644
--- a/src/resources/extensions/gsd/tests/derive-state-db.test.ts
+++ b/src/resources/extensions/gsd/tests/derive-state-db.test.ts
@@ -962,4 +962,37 @@ describe('derive-state-db', async () => {
       cleanup(base);
     }
   });
+
+  // ─── Regression: disk-only milestones synced into DB (#2416) ─────────
+  test('derive-state-db: disk-only milestone auto-synced into DB (#2416)', async () => {
+    const base = createFixtureBase();
+    try {
+      // M001 is complete and exists in DB. M002 was queued on disk only — no DB row.
+      writeFile(base, 'milestones/M001/M001-SUMMARY.md', '# M001 Summary\n\nDone.');
+      writeFile(base, 'milestones/M002/M002-CONTEXT.md', '# M002: Queued\n\nQueued milestone.');
+
+      openDatabase(':memory:');
+      // Only insert M001 — simulates the state after migration guard ran then /gsd queue added M002
+      insertMilestone({ id: 'M001', title: 'First', status: 'complete' });
+
+      invalidateStateCache();
+      const state = await deriveStateFromDb(base);
+
+      // Before the fix, M002 was invisible: getAllMilestones() returned only M001
+      // (complete) → phase='complete' → auto-mode stopped.
+      // After the fix, deriveStateFromDb reconciles disk dirs and inserts M002.
+      assert.deepStrictEqual(state.phase, 'pre-planning', 'disk-sync-2416: phase is pre-planning, not complete');
+      assert.deepStrictEqual(state.registry.length, 2, 'disk-sync-2416: both milestones visible in registry');
+      assert.deepStrictEqual(state.registry[0]?.id, 'M001', 'disk-sync-2416: registry[0] is M001');
+      assert.deepStrictEqual(state.registry[0]?.status, 'complete', 'disk-sync-2416: M001 is complete');
+      assert.deepStrictEqual(state.registry[1]?.id, 'M002', 'disk-sync-2416: registry[1] is M002');
+      assert.deepStrictEqual(state.registry[1]?.status, 'active', 'disk-sync-2416: M002 is active');
+      assert.deepStrictEqual(state.activeMilestone?.id, 'M002', 'disk-sync-2416: activeMilestone is M002');
+
+      closeDatabase();
+    } finally {
+      closeDatabase();
+      cleanup(base);
+    }
+  });
 });