diff --git a/packages/realm-server/tests/full-reindex-test.ts b/packages/realm-server/tests/full-reindex-test.ts
index cd3e798c0cd..34349dbd92a 100644
--- a/packages/realm-server/tests/full-reindex-test.ts
+++ b/packages/realm-server/tests/full-reindex-test.ts
@@ -87,7 +87,11 @@ module(basename(__filename), function (hooks) {
       realmUrls: [sourceRealmURL, publishedRealmURL],
     });
 
-    type JobArgs = { realmURL: string; realmUsername: string };
+    type JobArgs = {
+      realmURL: string;
+      realmUsername: string;
+      clearLastModified: boolean;
+    };
     type JobRow = {
       job_type: string;
       concurrency_group: string | null;
@@ -116,6 +120,12 @@ module(basename(__filename), function (hooks) {
       {
         realmURL: sourceRealmURL,
         realmUsername: 'owner',
+        // full-reindex enqueues with clearLastModified: true so every
+        // file re-renders even when its mtime is unchanged. Surfaced in
+        // args so the from-scratch coalesce can refuse to attach a
+        // clearing publish to an already-running same-realm
+        // from-scratch.
+        clearLastModified: true,
       },
       'source job args are correct',
     );
@@ -137,6 +147,7 @@ module(basename(__filename), function (hooks) {
       {
         realmURL: publishedRealmURL,
         realmUsername: 'owner',
+        clearLastModified: true,
       },
       'published job args use the source owner',
     );
diff --git a/packages/realm-server/tests/queue-test.ts b/packages/realm-server/tests/queue-test.ts
index db2f1661974..57ead25c539 100644
--- a/packages/realm-server/tests/queue-test.ts
+++ b/packages/realm-server/tests/queue-test.ts
@@ -54,7 +54,9 @@ module(basename(__filename), function () {
     });
 
     async function publishFromScratchIndexJob(args: {
-      args: FromScratchArgs;
+      args: Omit<FromScratchArgs, 'clearLastModified'> & {
+        clearLastModified?: boolean;
+      };
       priority: number;
     }) {
       return await publisher.publish<FromScratchResult>({
@@ -62,7 +64,7 @@ module(basename(__filename), function () {
         concurrencyGroup: `indexing:${args.args.realmURL}`,
         timeout: FROM_SCRATCH_JOB_TIMEOUT_SEC,
         priority: args.priority,
-        args: args.args,
+        args: { clearLastModified: false, ...args.args },
       });
     }
 
@@ -323,6 +325,170 @@ module(basename(__filename), function () {
       );
     });
 
+    test('from-scratch dedup: a duplicate publish for an in-flight from-scratch attaches as a late waiter', async function (assert) {
+      // From-scratch reindex is the maximal indexing operation for a
+      // realm: any same-realm from-scratch already running subsumes a
+      // second concurrent from-scratch by definition. A worker
+      // claiming the first publish before the second arrives must not
+      // force a second canonical row, because the second caller's
+      // result is already covered by what the in-flight job will
+      // produce.
+      await runner.destroy();
+      let realmURL = 'http://example.com/from-scratch-in-flight-dedup/';
+      let started = new Deferred<void>();
+      let release = new Deferred<void>();
+
+      let worker = new PgQueueRunner({
+        adapter,
+        workerId: 'from-scratch-in-flight-worker',
+      });
+      worker.register('from-scratch-index', async () => {
+        started.fulfill();
+        await release.promise;
+        return {
+          invalidations: [],
+          ignoreData: {},
+          stats: {
+            instancesIndexed: 0,
+            filesIndexed: 0,
+            instanceErrors: 0,
+            fileErrors: 0,
+            totalIndexEntries: 0,
+          },
+        };
+      });
+
+      try {
+        await worker.start();
+
+        let first = await publishFromScratchIndexJob({
+          priority: 0,
+          args: {
+            realmURL,
+            realmUsername: 'owner',
+          },
+        });
+        // Wait for the worker to actually claim the job — that moves
+        // the row from `candidates` to `inFlightCandidates`, which is
+        // the precondition for the pending-candidate path to miss and
+        // the in-flight fallback to fire.
+        await started.promise;
+
+        let second = await publishFromScratchIndexJob({
+          priority: userInitiatedPriority,
+          args: {
+            realmURL,
+            realmUsername: 'owner',
+          },
+        });
+
+        assert.strictEqual(
+          first.id,
+          second.id,
+          'duplicate publish reuses the in-flight job id instead of creating a new row',
+        );
+
+        let rows = (await adapter.execute(
+          `SELECT id
+             FROM jobs
+             WHERE concurrency_group = $1
+               AND status = 'unfulfilled'`,
+          { bind: [`indexing:${realmURL}`] },
+        )) as { id: number }[];
+        assert.strictEqual(
+          rows.length,
+          1,
+          'only one from-scratch-index row exists; duplicate did not enqueue a second job',
+        );
+
+        release.fulfill();
+        await Promise.all([first.done, second.done]);
+      } finally {
+        release.fulfill();
+        await worker.destroy();
+      }
+    });
+
+    test('from-scratch dedup: a clearLastModified publish does NOT attach to an in-flight from-scratch', async function (assert) {
+      // A clearLastModified publish has already nulled
+      // boxel_index.last_modified for the realm so the next from-scratch
+      // pass re-renders every row. An already-running from-scratch read
+      // its mtimes snapshot before that clear, so joining the running
+      // job would let the caller observe a successful job that did NOT
+      // re-render the swapped files (e.g. a publish-realm caller would
+      // return ok despite never having indexed the new content).
+      await runner.destroy();
+      let realmURL = 'http://example.com/from-scratch-clear-last-modified/';
+      let started = new Deferred<void>();
+      let release = new Deferred<void>();
+
+      let worker = new PgQueueRunner({
+        adapter,
+        workerId: 'from-scratch-clear-worker',
+      });
+      worker.register('from-scratch-index', async () => {
+        started.fulfill();
+        await release.promise;
+        return {
+          invalidations: [],
+          ignoreData: {},
+          stats: {
+            instancesIndexed: 0,
+            filesIndexed: 0,
+            instanceErrors: 0,
+            fileErrors: 0,
+            totalIndexEntries: 0,
+          },
+        };
+      });
+
+      try {
+        await worker.start();
+
+        let first = await publishFromScratchIndexJob({
+          priority: 0,
+          args: { realmURL, realmUsername: 'owner' },
+        });
+        await started.promise;
+
+        // Second publish flags clearLastModified — must not coalesce
+        // onto the running first job.
+        let second = await publishFromScratchIndexJob({
+          priority: userInitiatedPriority,
+          args: {
+            realmURL,
+            realmUsername: 'owner',
+            clearLastModified: true,
+          },
+        });
+
+        assert.notStrictEqual(
+          first.id,
+          second.id,
+          'clearLastModified publish does not attach to the in-flight job',
+        );
+
+        let rows = (await adapter.execute(
+          `SELECT id, status
+             FROM jobs
+             WHERE concurrency_group = $1
+             ORDER BY id`,
+          { bind: [`indexing:${realmURL}`] },
+        )) as { id: number; status: string }[];
+        assert.strictEqual(
+          rows.length,
+          2,
+          'a fresh row is inserted for the clearLastModified publish',
+        );
+
+        release.fulfill();
+        await Promise.all([first.done, second.done]);
+      } finally {
+        release.fulfill();
+        await worker.destroy();
+      }
+    });
+
     test('from-scratch does not coalesce onto pending incremental in same group', async function (assert) {
       await runner.destroy();
 
diff --git a/packages/realm-server/tests/server-endpoints/maintenance-endpoints-test.ts b/packages/realm-server/tests/server-endpoints/maintenance-endpoints-test.ts
index 3eed1d5a108..bc647748776 100644
--- a/packages/realm-server/tests/server-endpoints/maintenance-endpoints-test.ts
+++ b/packages/realm-server/tests/server-endpoints/maintenance-endpoints-test.ts
@@ -665,6 +665,12 @@ module(`server-endpoints/${basename(__filename)}`, function () {
           {
             realmURL,
             realmUsername: owner,
+            // The grafana reindex path passes clearLastModified: true so
+            // every file in boxel_index re-renders even when its mtime
+            // hasn't changed. Surfaced in args so the from-scratch
+            // coalesce can refuse to attach this kind of publish to an
+            // already-running same-realm from-scratch.
+            clearLastModified: true,
           },
           'realm args are correct',
         );
diff --git a/packages/runtime-common/jobs/reindex-realm.ts b/packages/runtime-common/jobs/reindex-realm.ts
index ceeda0b00ab..281aa24a855 100644
--- a/packages/runtime-common/jobs/reindex-realm.ts
+++ b/packages/runtime-common/jobs/reindex-realm.ts
@@ -17,11 +17,16 @@ export async function enqueueReindexRealmJob(
   priority: number,
   opts?: EnqueueReindexRealmJobOptions,
 ) {
+  // Flagging the args so the from-scratch coalesce can refuse to attach
+  // a forced-refresh publish to an already-running same-realm
+  // from-scratch whose mtimes snapshot pre-dates the clear below.
+  let clearLastModified = opts?.clearLastModified === true;
   let args = {
     realmURL: realmUrl,
     realmUsername,
+    clearLastModified,
   };
-  if (opts?.clearLastModified) {
+  if (clearLastModified) {
     await query(dbAdapter, [
       `UPDATE boxel_index SET last_modified = NULL WHERE realm_url =`,
       param(realmUrl),
diff --git a/packages/runtime-common/tasks/indexer.ts b/packages/runtime-common/tasks/indexer.ts
index 76bfd16eccc..aa8c584e6e2 100644
--- a/packages/runtime-common/tasks/indexer.ts
+++ b/packages/runtime-common/tasks/indexer.ts
@@ -55,7 +55,18 @@ export interface IncrementalDoneResult extends IncrementalResult {
   clientRequestId: string | null;
 }
 
-export type FromScratchArgs = WorkerArgs;
+export interface FromScratchArgs extends WorkerArgs {
+  // True when the caller cleared `boxel_index.last_modified` for the
+  // realm before publishing. The worker doesn't need to act on this
+  // (the clear already happened in the DB) — it's surfaced in args
+  // so the coalesce decision can refuse to attach a clearing publish
+  // to an already-running same-realm from-scratch whose
+  // `Batch.getModifiedTimes` snapshot pre-dates the clear, which would
+  // otherwise let the running job report success without re-rendering
+  // the swapped files. Always present (non-optional) so the args
+  // object satisfies WorkerArgs's JSON-shape index signature.
+  clearLastModified: boolean;
+}
 
 export interface FromScratchResult extends JSONTypes.Object {
   invalidations: string[];
@@ -239,29 +250,59 @@ function chooseIncrementalCoalesceDecision(
 function chooseFromScratchCoalesceDecision(
   context: QueueCoalesceContext,
 ): QueueCoalesceDecision {
-  let { incoming, candidates } = context;
+  let { incoming, candidates, inFlightCandidates } = context;
   let sameTypeCandidate = candidates.find(
     (candidate) => candidate.jobType === incoming.jobType,
   );
-  if (!sameTypeCandidate) {
-    return { type: 'insert' };
+  if (sameTypeCandidate) {
+    return {
+      type: 'join',
+      jobId: sameTypeCandidate.id,
+      update: {
+        ...maxPriorityAndTimeout(sameTypeCandidate, incoming),
+        args: {
+          ...(isObjectLike(sameTypeCandidate.args)
+            ? sameTypeCandidate.args
+            : {}),
+          ...(isObjectLike(incoming.args) ? incoming.args : {}),
+          coalescedCallers: mergeCoalescedCallers(
+            getCoalescedCallers(sameTypeCandidate.args),
+            getCoalescedCallers(incoming.args),
+          ),
+        },
+      },
+    };
   }
 
-  return {
-    type: 'join',
-    jobId: sameTypeCandidate.id,
-    update: {
-      ...maxPriorityAndTimeout(sameTypeCandidate, incoming),
-      args: {
-        ...(isObjectLike(sameTypeCandidate.args) ? sameTypeCandidate.args : {}),
-        ...(isObjectLike(incoming.args) ? incoming.args : {}),
-        coalescedCallers: mergeCoalescedCallers(
-          getCoalescedCallers(sameTypeCandidate.args),
-          getCoalescedCallers(incoming.args),
-        ),
-      },
-    },
-  };
+  // No still-pending candidate. Attach to an in-flight same-realm
+  // from-scratch instead — same concurrency group + same jobType is
+  // sufficient because a from-scratch reindex subsumes any other
+  // from-scratch for that realm by definition. Without this fallback,
+  // a worker claiming the first enqueue between two pre-claim publishes
+  // forces the second to insert a fresh row at its own priority, even
+  // though the in-flight job will produce exactly the result the second
+  // caller wanted.
+  //
+  // Exception: a publish carrying `clearLastModified: true` has already
+  // nulled `boxel_index.last_modified` for the realm so the next
+  // from-scratch pass re-renders every row even where mtimes didn't
+  // change. An already-running from-scratch read its mtimes snapshot
+  // before that clear, so attaching this publish to it would let the
+  // caller observe a successful job that did NOT actually re-render
+  // the swapped files. Force a fresh row instead.
+  if (!incomingClearsLastModified(incoming.args)) {
+    for (let candidate of inFlightCandidates) {
+      if (candidate.jobType === incoming.jobType) {
+        return { type: 'join', jobId: candidate.id };
+      }
+    }
+  }
+
+  return { type: 'insert' };
+}
+
+function incomingClearsLastModified(args: unknown): boolean {
+  return isObjectLike(args) && args.clearLastModified === true;
 }
 
 registerQueueJobDefinition({