diff --git a/gitnexus/src/core/run-analyze.ts b/gitnexus/src/core/run-analyze.ts
index a03122c2e..b144065a8 100644
--- a/gitnexus/src/core/run-analyze.ts
+++ b/gitnexus/src/core/run-analyze.ts
@@ -4614,9 +4614,11 @@ async function runFullAnalysisInner(
       // re-read the on-disk meta immediately before writing (the shape the
       // /api/embed checkpoint writer in server/api.ts already uses, which also
       // keeps a concurrent writer's update from being reverted by a stale
-      // snapshot) and replace ONLY `embeddingCheckpoint`. In-place writers
-      // can also publish a measured live count; staged writers keep it in
-      // memory until the replacement is published.
+      // snapshot) and replace ONLY `embeddingCheckpoint` — plus
+      // `stats.embeddings` when the caller actually MEASURED the published
+      // index (the post-window `onCheckpoint` on an in-place build). A staging
+      // build's count is not published until the atomic swap succeeds. The
+      // window-start callback passes nothing, preserving the latest count.
       const saveEmbeddingCheckpoint = async (
         checkpoint: {
           nodesProcessed: number;
@@ -4888,9 +4890,8 @@ async function runFullAnalysisInner(
     // already written to disk: prior meta says 0, a clean run inserts
     // embeddings and checkpoints the real count, the final probe is
     // unavailable, and finalization carries the stale 0 forward while reporting
-    // success. `loadMeta` never throws (it returns null), and the checkpoint
-    // writer already re-reads the same way, so this is the same freshness
-    // discipline applied to the same field.
+    // success. For a staged build, use its last measured count only in the
+    // final meta, written after the swap; never publish it at a checkpoint.
     const latestMetaForCount =
       embeddingCount === undefined ? ((await loadMeta(metaDir)) ?? existingMeta) : undefined;
     const persistedEmbeddingCount = resolvePersistedEmbeddingCount(
diff --git a/gitnexus/test/unit/run-analyze-fts-repair.test.ts b/gitnexus/test/unit/run-analyze-fts-repair.test.ts
index 6ebfd3c6f..5d616cf30 100644
--- a/gitnexus/test/unit/run-analyze-fts-repair.test.ts
+++ b/gitnexus/test/unit/run-analyze-fts-repair.test.ts
@@ -2321,15 +2321,14 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
             nodeIds: ['node-1', 'node-2'],
           });
           snapshots.windowStart = await loadMeta(storagePath);
-          // Post-window checkpoint — this one MEASURED the live count.
+          // Post-window checkpoint measures staging, not the published DB.
           await pipelineOptions.onCheckpoint?.({
             nodesProcessed: 2,
             totalNodes: 4,
             chunksProcessed: 4,
           });
           snapshots.postWindow = await loadMeta(storagePath);
-          // Window 2 — the old code restated the PREVIOUS run's count here and
-          // clobbered the live figure the post-window save had just written.
+          // Window 2 must retain the published count too.
           await pipelineOptions.onCheckpointWindowStart?.({
             nodesProcessed: 2,
             totalNodes: 4,
@@ -2381,7 +2380,7 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
       });
       expect(snapshots.windowStart?.lastCommit).not.toBe(currentCommit);
 
-      // The measured count belongs to the unpublished staging generation.
+      // ── Post-window: the staged count is not published yet ─────────────
       expect(snapshots.postWindow).toMatchObject({
         lastCommit: STALE_COMMIT,
         fileHashes: STALE_HASHES,
@@ -2394,7 +2393,7 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
         unsafeNodeIds: [],
       });
 
-      // ── Window 2: no stale restatement over the measured figure ────────
+      // ── Window 2: the published count remains unchanged ────────────────
       expect(snapshots.secondWindow).toMatchObject({
         lastCommit: STALE_COMMIT,
         stats: { embeddings: 7 },
@@ -2409,7 +2408,7 @@ describe('runFullAnalysis embedding-checkpoint meta write (#2790)', () => {
       const finalMeta = JSON.parse(
         await fs.readFile(`${storagePath}/meta.json`, 'utf-8'),
       ) as RepoMeta;
-      expect(finalMeta).toMatchObject({ lastCommit: currentCommit });
+      expect(finalMeta).toMatchObject({ lastCommit: currentCommit, stats: { embeddings: 42 } });
       expect(finalMeta.embeddingCheckpoint).toBeUndefined();
       expect(finalMeta.incrementalInProgress).toBeUndefined();
     } finally {