diff --git a/scripts/build/README.md b/scripts/build/README.md
index 074e83d754..7f5c2fde17 100644
--- a/scripts/build/README.md
+++ b/scripts/build/README.md
@@ -120,6 +120,10 @@ marker. Files, symlinks, and source directories are rejected. The exact npm
 destinations (`ui-tui/dist`, `hermes_cli/web_dist`, `apps/desktop/dist`, and
 `apps/desktop/build/native-deps`) remain rebuildable without a prior marker.
 Other in-tree products live beneath `.build/` or `apps/desktop/build/products/`.
+`frontend-common.mjs` classifies these destinations independently of which source
+children already exist, so a warm desktop rebuild uses the same rule as a fresh
+build. Explicit stamp, icon, native-tree and dependency inputs remain protected,
+even when they live beneath a generated destination.
 
 ### Icons and native inputs
 
diff --git a/scripts/build/desktop.mjs b/scripts/build/desktop.mjs
index e140bf5158..ddd650589e 100644
--- a/scripts/build/desktop.mjs
+++ b/scripts/build/desktop.mjs
@@ -29,9 +29,10 @@ export async function buildDesktop({ source, out, icons, stamp, nativeDeps, type
   if (!icons || !stamp || !nativeDeps) throw new Error('icons, stamp and nativeDeps are required prepared inputs')
   const app = 'apps/desktop'
   ;({ source, out } = productOutput(source, out, [
-    ...readdirSync(join(resolve(source), app)).filter(name => name !== 'dist').map(name => `${app}/${name}`),
-    `${app}/scripts`, 'scripts/build', 'package.json', 'package-lock.json',
-    'apps/shared', 'node_modules', ...[join(resolve(icons), app, 'public'), stamp, nativeDeps].map(input => relative(resolve(source), resolve(input))),
+    // productOutput owns source/generated classification. Protect prepared
+    // inputs explicitly, including dependency symlinks outside the checkout.
+    `${app}/node_modules`, 'node_modules',
+    ...[join(resolve(icons), app, 'public'), stamp, nativeDeps].map(input => relative(resolve(source), resolve(input))),
   ]))
   const publicIcons = join(resolve(icons), app, 'public')
   if (!existsSync(join(publicIcons, 'apple-touch-icon.png'))) throw new Error(`Missing desktop icon: ${join(publicIcons, 'apple-touch-icon.png')}`)
diff --git a/scripts/build/frontend-common.mjs b/scripts/build/frontend-common.mjs
index 2b2088f9ce..7a2284ef87 100644
--- a/scripts/build/frontend-common.mjs
+++ b/scripts/build/frontend-common.mjs
@@ -50,6 +50,9 @@ function requireOwnedOutput(out, source) {
   }
 }
 
+// Classify in-tree destinations here, not by enumerating existing workspace
+// children: generated parents also exist after the first build. inputs names
+// explicit prepared trees/files; their protection wins even in generated homes.
 export function productOutput(source, out, inputs) {
   if (!source || !out) throw new Error('source and output paths are required')
   const src = realpathSync(path.resolve(source))
diff --git a/tests-js/desktop-builder.test.mjs b/tests-js/desktop-builder.test.mjs
index ba93f804be..6eac116656 100644
--- a/tests-js/desktop-builder.test.mjs
+++ b/tests-js/desktop-builder.test.mjs
@@ -97,6 +97,31 @@ test('desktop compiler consumes explicit immutable inputs, replaces variants, an
   expect(files(input.source).some(([name]) => name.includes('.vite') || name.endsWith('tsbuildinfo'))).toBe(false)
 }, 60000)
 
+test('in-tree desktop products rebuild after build exists without replacing prepared inputs', async () => {
+  const { buildDesktop } = await import('../scripts/build/desktop.mjs')
+  const { productCurrent } = await import('../scripts/build/freshness.mjs')
+  const input = fixture()
+  input.out = join(input.source, 'apps/desktop/build/products/desktop')
+  await buildDesktop(input)
+  put(join(input.source, 'apps/desktop/src/index.js'), 'document.getElementById("app").textContent = "warm rebuild"')
+  await buildDesktop(input)
+  expect(productCurrent({ ...input, product: 'desktop' })).toBe(true)
+  const assets = files(join(input.out, 'assets')).map(([, bytes]) => Buffer.from(bytes, 'base64').toString()).join('')
+  expect(assets).toContain('warm rebuild')
+
+  // The generated-path allowance never overrides an explicitly prepared input,
+  // even when that input itself is an earlier builder-owned product.
+  const built = files(input.out)
+  for (const prepared of [
+    { stamp: join(input.out, 'hermes-build.json') },
+    { nativeDeps: join(input.out, 'node_modules') },
+    { icons: input.out },
+  ]) {
+    await expect(buildDesktop({ ...input, ...prepared })).rejects.toThrow(/overlap/)
+    expect(files(input.out)).toEqual(built)
+  }
+}, 30000)
+
 test('a prepared input changing during desktop compilation cannot publish a current receipt', async () => {
   const { buildDesktop } = await import('../scripts/build/desktop.mjs')
   const input = fixture()
@@ -137,7 +162,7 @@ test('typecheck uses scratch state and incomplete prepared inputs fail before pu
   rmSync(join(input.icons, 'apps/desktop/public/apple-touch-icon.png'))
   await expect(buildDesktop(input)).rejects.toThrow(/icon/i)
   expect(files(input.out)).toEqual(built)
-  await expect(buildDesktop({ ...input, out: join(input.source, 'apps/desktop/scripts') })).rejects.toThrow(/overlap/)
+  await expect(buildDesktop({ ...input, out: join(input.source, 'apps/desktop/scripts') })).rejects.toThrow(/Output/)
   put(join(input.icons, 'apps/desktop/public/apple-touch-icon.png'), 'fresh icon')
   rmSync(join(input.nativeDeps, 'node-pty/build'), { recursive: true, force: true })
   rmSync(join(input.nativeDeps, 'node-pty/prebuilds'), { recursive: true, force: true })