diff --git a/cli/src/commands/app/app_metadata.ts b/cli/src/commands/app/app_metadata.ts
index 8d5a812f7d..a1f524fbcd 100644
--- a/cli/src/commands/app/app_metadata.ts
+++ b/cli/src/commands/app/app_metadata.ts
@@ -472,8 +472,11 @@ async function updateRawAppRunnables(
     // Skip frontend scripts - they don't need locks
     if (language === "frontend") {
       // Still need to write the runnable YAML file
+      // Use runnableId (the dict key) for file naming, consistent with
+      // extractInlineScriptsForApps in sync.ts which also uses the key.
+      // Using runnable.name would create duplicate files when name != key.
       const [basePathO, ext] = pathAssigner.assignPath(
-        runnable.name ?? runnableId,
+        runnableId,
         language
       );
       const basePath = basePathO.replaceAll(SEP, "/");
@@ -509,8 +512,11 @@ async function updateRawAppRunnables(
       );
 
       // Determine file extension for this language
+      // Use runnableId (the dict key) for file naming, consistent with
+      // extractInlineScriptsForApps in sync.ts which also uses the key.
+      // Using runnable.name would create duplicate files when name != key.
       const [basePathO, ext] = pathAssigner.assignPath(
-        runnable.name ?? runnableId,
+        runnableId,
         language
       );
       const basePath = basePathO.replaceAll(SEP, "/");
diff --git a/cli/test/repro_diffname.test.ts b/cli/test/repro_diffname.test.ts
new file mode 100644
index 0000000000..83dcdc44a3
--- /dev/null
+++ b/cli/test/repro_diffname.test.ts
@@ -0,0 +1,114 @@
+import { test, expect } from "bun:test";
+import { writeFile, readdir } from "node:fs/promises";
+import path from "node:path";
+import { withTestBackend } from "./test_backend.ts";
+import { addWorkspace } from "../src/commands/workspace/workspace.ts";
+
+/**
+ * Regression test for duplicate backend scripts in raw apps.
+ *
+ * Root cause: updateRawAppRunnables (app_metadata.ts) used runnable.name for
+ * file naming while extractInlineScriptsForApps (sync.ts) used the runnable KEY.
+ * When name != key (common: keys are "a","b", names are "Fetch Users","Update Record"),
+ * generate-metadata created duplicate content files (e.g., fetch_users.ts alongside a.ts).
+ * On next push, loadRunnablesFromBackend auto-detected the orphans as new runnables.
+ */
+test("Raw app: generate-metadata must not create duplicate files when runnable key != name", async () => {
+  await withTestBackend(async (backend, tempDir) => {
+    const testWorkspace = {
+      remote: backend.baseUrl,
+      workspaceId: backend.workspace,
+      name: "diffname_test",
+      token: backend.token,
+    };
+    await addWorkspace(testWorkspace, { force: true, configDir: backend.testConfigDir });
+
+    await writeFile(
+      `${tempDir}/wmill.yaml`,
+      `defaultTs: bun\nincludes:\n  - "**"\nexcludes: []\n`,
+      "utf-8",
+    );
+
+    // Create raw app where runnable KEY differs from runnable NAME
+    const appPath = "f/test/diffname_app";
+    const rawAppJson = {
+      value: {
+        runnables: {
+          a: {
+            type: "runnableByName",
+            name: "Fetch Users",
+            inlineScript: {
+              content: 'export async function main(x: string) { return x; }',
+              language: "bun", lock: "",
+            },
+            fields: { x: { type: "static", value: "hello" } },
+          },
+          b: {
+            type: "runnableByName",
+            name: "Update Record",
+            inlineScript: {
+              content: 'export async function main(y: number) { return y * 2; }',
+              language: "bun", lock: "",
+            },
+            fields: { y: { type: "static", value: 42 } },
+          },
+        },
+        files: { "/index.tsx": "console.log('hello');" },
+      },
+      path: appPath,
+      summary: "Test Diffname App",
+      policy: { execution_mode: "publisher", triggerables: {} },
+    };
+
+    const formData = new FormData();
+    formData.append("app", new Blob([JSON.stringify(rawAppJson)], { type: "application/json" }));
+    formData.append("js", new Blob(["console.log('b');"], { type: "application/javascript" }));
+    formData.append("css", new Blob([".t{}"], { type: "text/css" }));
+
+    const createResp = await fetch(
+      `${backend.baseUrl}/api/w/${backend.workspace}/apps/create_raw`,
+      { method: "POST", headers: { Authorization: `Bearer ${backend.token}` }, body: formData },
+    );
+    expect(createResp.ok).toBeTruthy();
+
+    // Pull the app
+    const pullResult = await backend.runCLICommand(["sync", "pull", "--yes"], tempDir);
+    expect(pullResult.code).toEqual(0);
+
+    const backendDir = path.join(tempDir, "f/test/diffname_app.raw_app", "backend");
+    let files = await readdir(backendDir);
+
+    // After pull: files named by KEY (a, b)
+    expect(files.sort()).toEqual(["a.lock", "a.ts", "a.yaml", "b.lock", "b.ts", "b.yaml"]);
+
+    // Run generate-metadata — this previously created duplicate files named by NAME
+    const metaResult = await backend.runCLICommand(["generate-metadata", "--yes"], tempDir);
+    expect(metaResult.code).toEqual(0);
+
+    // After generate-metadata: must still only have KEY-based files, no NAME-based duplicates
+    files = await readdir(backendDir);
+    const tsFiles = files.filter(f => f.endsWith(".ts")).sort();
+
+    // Critical assertion: should be ["a.ts", "b.ts"], NOT ["a.ts", "b.ts", "fetch_users.ts", "update_record.ts"]
+    expect(tsFiles).toEqual(["a.ts", "b.ts"]);
+
+    // No orphaned name-based files should exist
+    expect(files).not.toContain("fetch_users.ts");
+    expect(files).not.toContain("update_record.ts");
+    expect(files).not.toContain("fetch_users.lock");
+    expect(files).not.toContain("update_record.lock");
+
+    // Push should be a no-op (no phantom changes)
+    const pushResult = await backend.runCLICommand(["sync", "push", "--yes"], tempDir);
+    expect(pushResult.code).toEqual(0);
+
+    // Backend should still have exactly 2 runnables
+    const getResp = await fetch(
+      `${backend.baseUrl}/api/w/${backend.workspace}/apps/get/p/${appPath}`,
+      { headers: { Authorization: `Bearer ${backend.token}` } },
+    );
+    const appAfterPush = await getResp.json() as any;
+    const runnables = appAfterPush.value?.runnables ?? {};
+    expect(Object.keys(runnables).length).toEqual(2);
+  });
+}, 180000);