diff --git a/src/core/brain-writer.ts b/src/core/brain-writer.ts
index a65e6864b..d7ff74082 100644
--- a/src/core/brain-writer.ts
+++ b/src/core/brain-writer.ts
@@ -409,6 +409,11 @@ export interface ScanOpts {
   visitDir?: (dirPath: string) => void;
 }
 
+/** Timeout-arm winner for the COUNT-vs-deadline race in scanBrainSources.
+ *  A unique object so it can never collide with a legitimate COUNT result
+ *  (number | null). Module-private. */
+const DEADLINE_SENTINEL: unique symbol = Symbol('gbrain.scan.deadline');
+
 export async function scanBrainSources(
   engine: BrainEngine,
   opts: ScanOpts = {},
@@ -480,41 +485,43 @@ export async function scanBrainSources(
     // pool can make this await hang past the budget. Without the race, we'd
     // wait indefinitely AND defeat the wall-clock guarantee.
     let dbPageCount: number | null = null;
+    // Set when the deadline race's timeout arm wins: the verdict that the
+    // budget is spent, independent of any later Date.now() reading. Timer
+    // callbacks on loaded runners can fire measurably EARLY relative to the
+    // wall clock (a +1ms pad was drifted past in practice — see the flake
+    // lineage in test/brain-writer-partial-scan.test.ts and issue #2946), so
+    // the hung-COUNT path must not re-derive "did the deadline fire?" from
+    // the clock the timer just raced against.
+    let deadlineHit = false;
     if (opts.dbPageCountForSource) {
       try {
         if (opts.deadline) {
           const remainingMs = opts.deadline - Date.now();
           if (remainingMs <= 0) {
             dbPageCount = null;
+            deadlineHit = true;
           } else {
-            // Race COUNT against the deadline so a hung query can't eat the budget.
-            //
-            // Boundary overshoot (+1ms): the post-await deadline check at line
-            // ~512 uses `Date.now() >= deadline`. setTimeout fires AT OR AFTER
-            // the requested delay, so in theory the check always passes. In
-            // practice on heavily-loaded CI runners (8 parallel shards × 4
-            // concurrent test files = ~32 concurrent bun processes) we saw
-            // intermittent failures where the timer callback resolved
-            // microseconds BEFORE the wall-clock boundary, leaving Date.now()
-            // a tick below deadline and the skip-check evaluating false. The
-            // src-a scan then ran on a populated dir before src-b's
-            // between-source check caught up — causing
-            // `firstSource.status === 'skipped'` to receive 'scanned'.
-            //
-            // Adding 1ms guarantees the timer fires past the deadline by at
-            // least one millisecond regardless of runner timer drift. Cost is
-            // 1ms additional wall-clock latency on hung COUNT queries, which
-            // is operationally negligible. Flake repro:
-            // https://github.com/garrytan/gbrain/actions/runs/77611667786
-            dbPageCount = await Promise.race([
+            // Race COUNT against the deadline so a hung query can't eat the
+            // budget. The timeout arm resolves a private sentinel — NOT null —
+            // so a deadline win is distinguishable from a COUNT that resolved
+            // null (failed/absent count keeps its existing semantics).
+            const raced = await Promise.race([
               opts.dbPageCountForSource(src.id),
-              new Promise<null>(resolve => setTimeout(() => resolve(null), remainingMs + 1)),
+              new Promise<typeof DEADLINE_SENTINEL>(resolve =>
+                setTimeout(() => resolve(DEADLINE_SENTINEL), remainingMs)),
             ]);
+            if (raced === DEADLINE_SENTINEL) {
+              dbPageCount = null;
+              deadlineHit = true;
+            } else {
+              dbPageCount = raced;
+            }
           }
         } else {
           dbPageCount = await opts.dbPageCountForSource(src.id);
         }
       } catch {
+        // A throwing COUNT is a failed count, not a deadline verdict.
         dbPageCount = null;
       }
     }
@@ -524,11 +531,11 @@ export async function scanBrainSources(
     // status='partial' with files_scanned=0, which is misleading ("partial
     // scan" when actually nothing was scanned). Mark this source + remainder
     // as 'skipped' so the doctor message is honest.
-    // `>=` matches the between-source check above (line 445). The Promise.race
-    // setTimeout resolves null at exactly `remainingMs` from now, so post-await
-    // Date.now() often equals deadline within integer-ms precision — strict `>`
-    // missed those landings on CI and let the next scanOneSource run anyway.
-    if (opts.signal?.aborted || (opts.deadline && Date.now() >= opts.deadline)) {
+    // `deadlineHit` is the authoritative verdict for the hung-COUNT path (the
+    // sentinel above); the wall-clock re-check (`>=`, matching the
+    // between-source check at line ~445) still covers a COUNT that RESOLVED
+    // slowly enough to eat the budget without the timer winning.
+    if (opts.signal?.aborted || deadlineHit || (opts.deadline && Date.now() >= opts.deadline)) {
       if (abortedAtSource === null) {
         abortedAtSource = src.id;
       }
diff --git a/test/brain-writer-partial-scan.test.ts b/test/brain-writer-partial-scan.test.ts
index 611c98dc6..e9b780134 100644
--- a/test/brain-writer-partial-scan.test.ts
+++ b/test/brain-writer-partial-scan.test.ts
@@ -174,6 +174,21 @@ describe('scanBrainSources partial-scan state', () => {
     expect(report.aborted_at_source).toBe('src-a');
   });
 
+  // #2946: the deadline race's timeout arm resolves a SENTINEL, not null —
+  // a COUNT that legitimately resolves null (failed/absent count) before the
+  // deadline must NOT be mistaken for a deadline hit: the source still gets
+  // scanned, with db_page_count simply unavailable.
+  test('COUNT resolving null before the deadline is not a deadline verdict — source still scans', async () => {
+    const start = Date.now();
+    const report = await scanBrainSources(engine, {
+      deadline: start + 5_000,
+      dbPageCountForSource: async () => null,
+    });
+    const firstSource = report.per_source.find(r => r.source_id === 'src-a')!;
+    expect(firstSource.status).toBe('scanned');
+    expect(firstSource.db_page_count == null).toBe(true);
+  });
+
   // Codex adversarial #4 regression: even when dbPageCountForSource itself
   // would hang indefinitely, the Promise.race against the deadline must
   // resolve null and the scan must abort cleanly.