diff --git a/scripts/smoke-test.mjs b/scripts/smoke-test.mjs
index cee6904..a6437e8 100644
--- a/scripts/smoke-test.mjs
+++ b/scripts/smoke-test.mjs
@@ -60,6 +60,21 @@ const fileContents = new Map([
   ["package.json", "{\n  \"name\": \"ide-smoke\"\n}\n"],
 ]);
 
+const indexedOnlyFileMetadata = new Map([
+  [
+    "deep/Nested.ts",
+    {
+      path: "deep/Nested.ts",
+      name: "Nested.ts",
+      parent: "deep",
+      isDir: false,
+      depth: 1,
+      size: 42,
+      modifiedMs: 5,
+    },
+  ],
+]);
+
 function findBrowserExecutable() {
   const candidates = [
     process.env.IDE_SMOKE_BROWSER,
@@ -143,7 +158,9 @@ async function fulfillApi(route) {
 
   if (url.pathname === "/api/file-metadata") {
     const filePath = url.searchParams.get("path") ?? "";
-    const entry = files.find((candidate) => candidate.path === filePath);
+    const entry =
+      files.find((candidate) => candidate.path === filePath) ??
+      indexedOnlyFileMetadata.get(filePath);
     if (entry) {
       await route.fulfill(json(entry));
     } else {
diff --git a/src/App.test.tsx b/src/App.test.tsx
index 3010a89..61b1470 100644
--- a/src/App.test.tsx
+++ b/src/App.test.tsx
@@ -271,8 +271,15 @@ describe("App shell interactions", () => {
     );
     tauriMocks.statFile.mockImplementation(async (path: string) => {
       const entry = files.find((candidate) => candidate.path === path);
-      if (!entry) throw new Error(`missing ${path}`);
-      return entry;
+      if (entry) return entry;
+      return {
+        path,
+        name: path.split("/").at(-1) ?? path,
+        isDir: false,
+        depth: path.split("/").length - 1,
+        size: 0,
+        modifiedMs: 0,
+      };
     });
     tauriMocks.recordRecentFile.mockResolvedValue(undefined);
     tauriMocks.readFile.mockImplementation(async (path: string) => {
@@ -2779,6 +2786,9 @@ describe("App shell interactions", () => {
     fireEvent.click(screen.getByTitle("Save"));
 
     await screen.findByText("Error: file changed on disk since it was opened");
+    expect(screen.getByRole("alert")).toHaveTextContent(
+      "Error: file changed on disk since it was opened",
+    );
     expect(tauriMocks.writeFile).toHaveBeenCalledWith(
       "README.md",
       "changed readme",
@@ -2788,6 +2798,42 @@ describe("App shell interactions", () => {
     expect(screen.getByText("Save failed")).toBeInTheDocument();
   });
 
+  it("saves with fresh metadata after opening a file from a stale tree entry", async () => {
+    const openOrder: string[] = [];
+    tauriMocks.statFile.mockImplementation(async (path: string) => {
+      const entry = files.find((candidate) => candidate.path === path);
+      if (!entry) throw new Error(`missing ${path}`);
+      if (path === "README.md") openOrder.push("stat");
+      return path === "README.md" ? { ...entry, modifiedMs: 303 } : entry;
+    });
+    tauriMocks.readFile.mockImplementation(async (path: string) => {
+      if (path === "README.md") {
+        openOrder.push("read");
+        return "readme";
+      }
+      if (path === "src/App.tsx") return "export function App() {}";
+      return "";
+    });
+    render(<App />);
+
+    fireEvent.click(await treeButton("README.md"));
+    await findTab("README.md");
+    expect(openOrder).toEqual(["stat", "read"]);
+    fireEvent.change(await screen.findByLabelText("Editor README.md"), {
+      target: { value: "changed readme" },
+    });
+
+    fireEvent.click(screen.getByTitle("Save"));
+
+    await waitFor(() =>
+      expect(tauriMocks.writeFile).toHaveBeenCalledWith(
+        "README.md",
+        "changed readme",
+        303,
+      ),
+    );
+  });
+
   it("reloads a clean active file from disk", async () => {
     render(<App />);
 
@@ -3571,7 +3617,6 @@ describe("App shell interactions", () => {
 
     await screen.findByText("Error: permission denied");
     expect(screen.getByRole("alertdialog", { name: "Delete file?" })).toBeInTheDocument();
-    expect(screen.getByText("Delete failed")).toBeInTheDocument();
   });
 });
 
diff --git a/src/App.tsx b/src/App.tsx
index bd78056..5557f9c 100644
--- a/src/App.tsx
+++ b/src/App.tsx
@@ -1075,6 +1075,12 @@ export default function App() {
     }
   }, [refreshFiles]);
 
+  const readOpenFileFromDisk = useCallback(async (path: string) => {
+    const entry = await statFile(path);
+    const contents = await readFile(path, maxOpenFileKb * 1024);
+    return { contents, modifiedMs: entry.modifiedMs };
+  }, [maxOpenFileKb]);
+
   const refreshWorkspaceIndexStats = useCallback(async () => {
     try {
       setWorkspaceIndexStats(await getWorkspaceIndexStats());
@@ -1262,13 +1268,13 @@ export default function App() {
       }
 
       try {
-        const contents = await readFile(entry.path, maxOpenFileKb * 1024);
+        const diskFile = await readOpenFileFromDisk(entry.path);
         setOpenFiles((current) =>
           addPreviewTab(current, {
             path: entry.path,
-            contents,
+            contents: diskFile.contents,
             dirty: false,
-            modifiedMs: entry.modifiedMs,
+            modifiedMs: diskFile.modifiedMs,
             pinned,
           }),
         );
@@ -1285,7 +1291,7 @@ export default function App() {
         setStatus("Open failed");
       }
     },
-    [maxOpenFileKb, openFiles, singleFileMode, trackActiveFile],
+    [openFiles, readOpenFileFromDisk, singleFileMode, trackActiveFile],
   );
 
   useEffect(() => {
@@ -1355,14 +1361,14 @@ export default function App() {
     let disposed = false;
     Promise.all(
       restorePaths.map(async (path) => {
-        const entry = entriesByPath.get(path)!;
         try {
+          const diskFile = await readOpenFileFromDisk(path);
           return {
             tab: {
               path,
-              contents: await readFile(path, maxOpenFileKb * 1024),
+              contents: diskFile.contents,
               dirty: false,
-              modifiedMs: entry.modifiedMs,
+              modifiedMs: diskFile.modifiedMs,
               pinned: true,
             },
           };
@@ -1429,7 +1435,7 @@ export default function App() {
     };
   }, [
     files,
-    maxOpenFileKb,
+    readOpenFileFromDisk,
     singleFileMode,
     uiStateLoaded,
     workspaceLoadFailed,
@@ -1838,17 +1844,15 @@ export default function App() {
     setStatus(`Saving ${fileToSave.path}`);
     try {
       await writeFile(fileToSave.path, fileToSave.contents, fileToSave.modifiedMs);
-      const refreshedEntries = await refreshFiles();
-      const modifiedMs = refreshedEntries.find(
-        (entry) => entry.path === fileToSave.path,
-      )?.modifiedMs;
+      const savedEntry = await statFile(fileToSave.path);
       setOpenFiles((current) =>
         current.map((file) =>
           file.path === fileToSave.path && file.contents === fileToSave.contents
-            ? { ...file, dirty: false, modifiedMs }
+            ? { ...file, dirty: false, modifiedMs: savedEntry.modifiedMs }
             : file,
         ),
       );
+      await refreshFiles();
       setStatus("Saved");
       return true;
     } catch (reason) {
@@ -1913,17 +1917,16 @@ export default function App() {
     setError(undefined);
     setStatus(`Reloading ${path}`);
     try {
-      const contents = await readFile(path, maxOpenFileKb * 1024);
-      const refreshedEntries = await refreshFiles();
-      const modifiedMs = refreshedEntries.find((entry) => entry.path === path)?.modifiedMs;
+      const diskFile = await readOpenFileFromDisk(path);
+      await refreshFiles();
       setOpenFiles((current) =>
         current.map((file) =>
           file.path === path
             ? {
                 ...file,
-                contents,
+                contents: diskFile.contents,
                 dirty: false,
-                modifiedMs,
+                modifiedMs: diskFile.modifiedMs,
               }
             : file,
         ),
@@ -1938,7 +1941,7 @@ export default function App() {
       setStatus("Reload failed");
       return false;
     }
-  }, [refreshFiles]);
+  }, [readOpenFileFromDisk, refreshFiles]);
 
   const requestReloadActiveFile = useCallback(() => {
     if (!activeFile) {
@@ -4994,7 +4997,12 @@ export default function App() {
         </div>
       ) : null}
 
-      {error ? <div className="toast">{error}</div> : null}
+      {error ? (
+        <div className="toast" role="alert">
+          <TriangleAlert size={16} aria-hidden="true" />
+          <span>{error}</span>
+        </div>
+      ) : null}
     </main>
   );
 }
diff --git a/src/styles.css b/src/styles.css
index c19a28e..5751b8d 100644
--- a/src/styles.css
+++ b/src/styles.css
@@ -1060,11 +1060,15 @@ button {
 
 .toast {
   position: fixed;
+  top: 14px;
   right: 16px;
-  bottom: 38px;
+  z-index: 50;
+  display: flex;
+  align-items: flex-start;
+  gap: 8px;
   max-width: min(520px, calc(100vw - 32px));
   padding: 10px 12px;
-  border: 1px solid var(--accent);
+  border: 1px solid var(--danger);
   border-radius: 6px;
   background: var(--panel);
   box-shadow: var(--shadow);
@@ -1072,6 +1076,12 @@ button {
   font-size: 13px;
 }
 
+.toast svg {
+  flex: 0 0 auto;
+  margin-top: 1px;
+  color: var(--danger);
+}
+
 .quick-open {
   position: fixed;
   inset: 0;