diff --git a/src/core/init.ts b/src/core/init.ts
index ab3dc55b..05e9be42 100644
--- a/src/core/init.ts
+++ b/src/core/init.ts
@@ -428,9 +428,11 @@ export class InitCommand {
     } else {
       ora({ stream: process.stdout }).info(
         PALETTE.midGray(
-          'ℹ OpenSpec already initialized. Skipping base scaffolding.'
+          'ℹ OpenSpec already initialized. Checking for missing files...'
         )
       );
+      await this.createDirectoryStructure(openspecPath);
+      await this.ensureTemplateFiles(openspecPath, config);
     }
 
     // Step 2: Configure AI tools
@@ -719,6 +721,21 @@ export class InitCommand {
   private async generateFiles(
     openspecPath: string,
     config: OpenSpecConfig
+  ): Promise<void> {
+    await this.writeTemplateFiles(openspecPath, config, false);
+  }
+
+  private async ensureTemplateFiles(
+    openspecPath: string,
+    config: OpenSpecConfig
+  ): Promise<void> {
+    await this.writeTemplateFiles(openspecPath, config, true);
+  }
+
+  private async writeTemplateFiles(
+    openspecPath: string,
+    config: OpenSpecConfig,
+    skipExisting: boolean
   ): Promise<void> {
     const context: ProjectContext = {
       // Could be enhanced with prompts for project details
@@ -728,6 +745,12 @@ export class InitCommand {
 
     for (const template of templates) {
       const filePath = path.join(openspecPath, template.path);
+
+      // Skip if file exists and we're in skipExisting mode
+      if (skipExisting && (await FileSystemUtils.fileExists(filePath))) {
+        continue;
+      }
+
       const content =
         typeof template.content === 'function'
           ? template.content(context)
diff --git a/test/core/init.test.ts b/test/core/init.test.ts
index 4c7a91d4..b6d8e35e 100644
--- a/test/core/init.test.ts
+++ b/test/core/init.test.ts
@@ -579,6 +579,44 @@ describe('InitCommand', () => {
       await expect(initCommand.execute(testDir)).resolves.toBeUndefined();
     });
 
+    it('should recreate deleted openspec/AGENTS.md in extend mode', async () => {
+      await testFileRecreationInExtendMode(
+        testDir,
+        initCommand,
+        'openspec/AGENTS.md',
+        'OpenSpec Instructions'
+      );
+    });
+
+    it('should recreate deleted openspec/project.md in extend mode', async () => {
+      await testFileRecreationInExtendMode(
+        testDir,
+        initCommand,
+        'openspec/project.md',
+        'Project Context'
+      );
+    });
+
+    it('should preserve existing template files in extend mode', async () => {
+      queueSelections('claude', DONE, DONE);
+
+      // First init
+      await initCommand.execute(testDir);
+
+      const agentsPath = path.join(testDir, 'openspec', 'AGENTS.md');
+      const customContent = '# My Custom AGENTS Content\nDo not overwrite this!';
+
+      // Modify the file with custom content
+      await fs.writeFile(agentsPath, customContent);
+
+      // Run init again - should NOT overwrite
+      await initCommand.execute(testDir);
+
+      const content = await fs.readFile(agentsPath, 'utf-8');
+      expect(content).toBe(customContent);
+      expect(content).not.toContain('OpenSpec Instructions');
+    });
+
     it('should handle non-existent target directory', async () => {
       queueSelections('claude', DONE);
 
@@ -1160,6 +1198,32 @@ describe('InitCommand', () => {
   });
 });
 
+async function testFileRecreationInExtendMode(
+  testDir: string,
+  initCommand: InitCommand,
+  relativePath: string,
+  expectedContent: string
+): Promise<void> {
+  queueSelections('claude', DONE, DONE);
+
+  // First init
+  await initCommand.execute(testDir);
+
+  const filePath = path.join(testDir, relativePath);
+  expect(await fileExists(filePath)).toBe(true);
+
+  // Delete the file
+  await fs.unlink(filePath);
+  expect(await fileExists(filePath)).toBe(false);
+
+  // Run init again - should recreate the file
+  await initCommand.execute(testDir);
+  expect(await fileExists(filePath)).toBe(true);
+
+  const content = await fs.readFile(filePath, 'utf-8');
+  expect(content).toContain(expectedContent);
+}
+
 async function fileExists(filePath: string): Promise<boolean> {
   try {
     await fs.access(filePath);