diff --git a/apps/daemon/src/projects.ts b/apps/daemon/src/projects.ts
index 8ce69f39e..f7c804aaa 100644
--- a/apps/daemon/src/projects.ts
+++ b/apps/daemon/src/projects.ts
@@ -32,10 +32,16 @@ const FORBIDDEN_SEGMENT = /^$|^\.\.?$/;
 const RESERVED_PROJECT_FILE_SEGMENTS = new Set(['.live-artifacts']);
 const DESIGN_HANDOFF_FILENAME = 'DESIGN-HANDOFF.md';
 const DESIGN_MANIFEST_FILENAME = 'DESIGN-MANIFEST.json';
+export const RUN_ARTIFACT_RECONCILE_MTIME_GRACE_MS = 1000;
 export const projectFileRenameTestHooks = {
   beforeCommit: null as null | ((paths: { source: string; target: string }) => Promise<void> | void),
 };
 
+export function isRunTouchedProjectFile(fileMtimeMs, runStartTimeMs) {
+  if (!Number.isFinite(fileMtimeMs) || !Number.isFinite(runStartTimeMs)) return false;
+  return fileMtimeMs + RUN_ARTIFACT_RECONCILE_MTIME_GRACE_MS >= runStartTimeMs;
+}
+
 export function projectDir(projectsRoot, projectId) {
   if (!isSafeId(projectId)) throw new Error('invalid project id');
   return path.join(projectsRoot, projectId);
diff --git a/apps/daemon/src/server.ts b/apps/daemon/src/server.ts
index 797caaf85..c254faa51 100644
--- a/apps/daemon/src/server.ts
+++ b/apps/daemon/src/server.ts
@@ -353,6 +353,7 @@ import {
   assertSandboxProjectRootAvailable,
   detectEntryFile,
   ensureProject,
+  isRunTouchedProjectFile,
   isSafeId,
   listFiles,
   mimeFor,
@@ -12751,7 +12752,7 @@ export async function startServer({
               try {
                 const filePath = path.join(dir, f.name);
                 const st = await fs.promises.stat(filePath);
-                if (st.mtimeMs < runStartTimeMs) continue;
+                if (!isRunTouchedProjectFile(st.mtimeMs, runStartTimeMs)) continue;
                 await reconcileHtmlArtifactManifest(
                   PROJECTS_DIR,
                   run.projectId,
diff --git a/apps/daemon/tests/artifact-manifest-reconcile-on-run-end.test.ts b/apps/daemon/tests/artifact-manifest-reconcile-on-run-end.test.ts
index 885f977c7..fbbe80c7b 100644
--- a/apps/daemon/tests/artifact-manifest-reconcile-on-run-end.test.ts
+++ b/apps/daemon/tests/artifact-manifest-reconcile-on-run-end.test.ts
@@ -9,7 +9,7 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { closeDatabase, insertProject, openDatabase } from '../src/db.js';
-import { reconcileHtmlArtifactManifest, writeProjectFile } from '../src/projects.js';
+import { isRunTouchedProjectFile, reconcileHtmlArtifactManifest, writeProjectFile } from '../src/projects.js';
 
 const PROJECT_ID = 'reconcile-test';
 let tempDir = null;
@@ -146,6 +146,9 @@ describe('run-end artifact manifest reconciliation (#2893)', () => {
 
     // File written during the run
     await writeProjectFile(projectsRoot, PROJECT_ID, 'new-output.html', '<p>new</p>');
+    const newPath = path.join(projectsRoot, PROJECT_ID, 'new-output.html');
+    const coarseFsTime = new Date(runStartTimeMs - 500);
+    fs.utimesSync(newPath, coarseFsTime, coarseFsTime);
 
     // Simulate the close-handler reconciliation with mtime filter
     const dir = path.join(projectsRoot, PROJECT_ID);
@@ -154,7 +157,7 @@ describe('run-end artifact manifest reconciliation (#2893)', () => {
       const ext = path.extname(name).toLowerCase();
       if (ext !== '.html' && ext !== '.htm') continue;
       const st = fs.statSync(path.join(dir, name));
-      if (st.mtimeMs < runStartTimeMs) continue;
+      if (!isRunTouchedProjectFile(st.mtimeMs, runStartTimeMs)) continue;
       await reconcileHtmlArtifactManifest(projectsRoot, PROJECT_ID, name);
     }