diff --git a/src/lib/packaging/__tests__/helpers.test.ts b/src/lib/packaging/__tests__/helpers.test.ts
index a554edb0e..4b830ed41 100644
--- a/src/lib/packaging/__tests__/helpers.test.ts
+++ b/src/lib/packaging/__tests__/helpers.test.ts
@@ -475,44 +475,68 @@ describe('nested agentcore directory is preserved (issue #843)', () => {
     expect(existsSync(join(dest, 'lib', 'langgraph_checkpoint_aws', 'agentcore', '__init__.py'))).toBe(true);
     expect(existsSync(join(dest, 'lib', 'langgraph_checkpoint_aws', 'agentcore', 'core.py'))).toBe(true);
   });
+});
+
+// ── Issue #1408: zip stage must not drop top-level agentcore Python packages ──
+
+describe('top-level agentcore Python package is preserved in zip (issue #1408)', () => {
+  let root: string;
+
+  beforeAll(() => {
+    root = mkdtempSync(join(tmpdir(), 'helpers-zip-agentcore-pkg-'));
+  });
 
-  // ── createZipFromDir (async) ──
+  afterAll(() => {
+    rmSync(root, { recursive: true, force: true });
+  });
 
-  it('zip: excludes top-level agentcore/ but includes nested agentcore/', async () => {
-    const src = buildFixture(join(root, 'zip-async'));
+  /**
+   * Mimics a staging directory after `uv pip install --target staging`
+   * has installed a third-party package whose top-level module happens to
+   * be named `agentcore`. The zip stage runs against staging, where the
+   * project's own `agentcore/` config dir is already absent, so a
+   * top-level `agentcore/` here is a real Python package and must be
+   * included in the deployment artifact.
+   */
+  function buildStagingFixture(base: string): string {
+    const staging = join(base, 'staging');
+
+    mkdirSync(staging, { recursive: true });
+    writeFileSync(join(staging, 'main.py'), 'print("hello")');
+
+    // Top-level `agentcore` Python package (e.g. an installed dependency)
+    mkdirSync(join(staging, 'agentcore'), { recursive: true });
+    writeFileSync(join(staging, 'agentcore', '__init__.py'), '# package init');
+    writeFileSync(join(staging, 'agentcore', 'runtime.py'), 'def run(): pass');
+
+    return staging;
+  }
+
+  it('createZipFromDir includes a top-level agentcore Python package', async () => {
+    const staging = buildStagingFixture(join(root, 'zip-async'));
     const zipPath = join(root, 'zip-async.zip');
 
-    await createZipFromDir(src, zipPath);
+    await createZipFromDir(staging, zipPath);
 
     const zipBuffer = await readFile(zipPath);
     const entries = Object.keys(unzipSync(new Uint8Array(zipBuffer)));
 
-    // Top-level agentcore/ should NOT appear
-    expect(entries.some(e => e === 'agentcore/config.yaml')).toBe(false);
-    expect(entries.some(e => e.startsWith('agentcore/'))).toBe(false);
-
-    // Nested agentcore/ SHOULD appear
-    expect(entries).toContain('lib/langgraph_checkpoint_aws/agentcore/__init__.py');
-    expect(entries).toContain('lib/langgraph_checkpoint_aws/agentcore/core.py');
-
-    // Regular files present
+    expect(entries).toContain('agentcore/__init__.py');
+    expect(entries).toContain('agentcore/runtime.py');
     expect(entries).toContain('main.py');
   });
 
-  // ── createZipFromDirSync ──
-
-  it('sync zip: excludes top-level agentcore/ but includes nested agentcore/', () => {
-    const src = buildFixture(join(root, 'zip-sync'));
+  it('createZipFromDirSync includes a top-level agentcore Python package', () => {
+    const staging = buildStagingFixture(join(root, 'zip-sync'));
     const zipPath = join(root, 'zip-sync.zip');
 
-    createZipFromDirSync(src, zipPath);
+    createZipFromDirSync(staging, zipPath);
 
     const zipBuffer = readFileSync(zipPath);
     const entries = Object.keys(unzipSync(new Uint8Array(zipBuffer)));
 
-    expect(entries.some(e => e.startsWith('agentcore/'))).toBe(false);
-    expect(entries).toContain('lib/langgraph_checkpoint_aws/agentcore/__init__.py');
-    expect(entries).toContain('lib/langgraph_checkpoint_aws/agentcore/core.py');
+    expect(entries).toContain('agentcore/__init__.py');
+    expect(entries).toContain('agentcore/runtime.py');
     expect(entries).toContain('main.py');
   });
 });
diff --git a/src/lib/packaging/helpers.ts b/src/lib/packaging/helpers.ts
index caa3d3792..7a0d72557 100644
--- a/src/lib/packaging/helpers.ts
+++ b/src/lib/packaging/helpers.ts
@@ -192,24 +192,23 @@ export async function createZipFromDir(sourceDir: string, outputZip: string): Pr
   await rm(outputZip, { force: true });
   await mkdir(dirname(outputZip), { recursive: true });
 
-  const files = await collectFiles(sourceDir, sourceDir);
+  const files = await collectFiles(sourceDir);
   const zipped = zipSync(files);
   await writeFile(outputZip, zipped);
 }
 
-async function collectFiles(directory: string, rootDir: string, basePath = ''): Promise<Zippable> {
+async function collectFiles(directory: string, basePath = ''): Promise<Zippable> {
   const result: Zippable = {};
   const entries = await readdir(directory, { withFileTypes: true });
 
   for (const entry of entries) {
     if (EXCLUDED_ENTRIES.has(entry.name)) continue;
-    if (entry.name === CONFIG_DIR && resolve(directory) === resolve(rootDir)) continue;
 
     const fullPath = join(directory, entry.name);
     const zipPath = basePath ? `${basePath}/${entry.name}` : entry.name;
 
     if (entry.isDirectory()) {
-      Object.assign(result, await collectFiles(fullPath, rootDir, zipPath));
+      Object.assign(result, await collectFiles(fullPath, zipPath));
     } else if (entry.isFile()) {
       result[zipPath] = [await readFile(fullPath), { level: 6 }];
     }
@@ -398,19 +397,18 @@ export function ensureBinaryAvailableSync(binary: string, installHint?: string):
   throw new MissingDependencyError(binary, installHint);
 }
 
-function collectFilesSync(directory: string, rootDir: string, basePath = ''): Zippable {
+function collectFilesSync(directory: string, basePath = ''): Zippable {
   const result: Zippable = {};
   const entries = readdirSync(directory, { withFileTypes: true });
 
   for (const entry of entries) {
     if (EXCLUDED_ENTRIES.has(entry.name)) continue;
-    if (entry.name === CONFIG_DIR && resolve(directory) === resolve(rootDir)) continue;
 
     const fullPath = join(directory, entry.name);
     const zipPath = basePath ? `${basePath}/${entry.name}` : entry.name;
 
     if (entry.isDirectory()) {
-      Object.assign(result, collectFilesSync(fullPath, rootDir, zipPath));
+      Object.assign(result, collectFilesSync(fullPath, zipPath));
     } else if (entry.isFile()) {
       result[zipPath] = [readFileSync(fullPath), { level: 6 }];
     }
@@ -422,7 +420,7 @@ export function createZipFromDirSync(sourceDir: string, outputZip: string): void
   rmSync(outputZip, { force: true });
   mkdirSync(dirname(outputZip), { recursive: true });
 
-  const files = collectFilesSync(sourceDir, sourceDir);
+  const files = collectFilesSync(sourceDir);
   const zipped = zipSync(files);
   writeFileSync(outputZip, zipped);
 }