diff --git a/src/server/__tests__/sessions.test.ts b/src/server/__tests__/sessions.test.ts
index faf89d71..cfed5ae9 100644
--- a/src/server/__tests__/sessions.test.ts
+++ b/src/server/__tests__/sessions.test.ts
@@ -932,6 +932,45 @@ describe('SessionService', () => {
     await expect(fs.access(worktreeFile)).resolves.toBeNull()
   })
 
+  it('should move repository metadata to the CLI worktree transcript before deleting placeholders', async () => {
+    const workDir = await createCleanGitRepo(tmpDir)
+    const { sessionId } = await service.createSession(
+      workDir,
+      { branch: 'main', worktree: true },
+    )
+    const initialLaunchInfo = await service.getSessionLaunchInfo(sessionId)
+    const worktreePath = initialLaunchInfo?.repository?.worktreePath
+    expect(worktreePath).toBeTruthy()
+
+    const worktreeFile = await writeSessionFile(sanitizePath(worktreePath!), sessionId, [
+      makeSnapshotEntry(),
+      {
+        type: 'system',
+        subtype: 'init',
+        cwd: worktreePath,
+        timestamp: '2026-01-01T00:00:01.000Z',
+      },
+      makeUserEntry('Hello from worktree'),
+    ])
+
+    await service.appendSessionMetadata(sessionId, {
+      workDir: worktreePath!,
+    })
+    const removed = await service.deletePlaceholderSessionFiles(sessionId, worktreePath!)
+    const launchInfo = await service.getSessionLaunchInfo(sessionId)
+
+    expect(removed).toBe(1)
+    await expect(fs.access(worktreeFile)).resolves.toBeNull()
+    expect(launchInfo?.workDir).toBe(worktreePath)
+    expect(launchInfo?.repository).toMatchObject({
+      requestedWorkDir: await fs.realpath(workDir),
+      branch: 'main',
+      worktree: true,
+      worktreePath,
+      worktreeSlug: initialLaunchInfo?.repository?.worktreeSlug,
+    })
+  })
+
   it('should recover workDir from transcript cwd when session-meta is missing', async () => {
     const sessionId = 'aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee'
     await writeSessionFile('-tmp-project', sessionId, [
diff --git a/src/server/services/conversationService.ts b/src/server/services/conversationService.ts
index 97c1ab43..a511eec8 100644
--- a/src/server/services/conversationService.ts
+++ b/src/server/services/conversationService.ts
@@ -520,6 +520,12 @@ export class ConversationService {
     return session?.workDir || ''
   }
 
+  updateSessionWorkDir(sessionId: string, workDir: string): void {
+    const session = this.sessions.get(sessionId)
+    if (!session || !workDir.trim()) return
+    session.workDir = workDir
+  }
+
   getSessionPermissionMode(sessionId: string): string {
     const session = this.sessions.get(sessionId)
     return session?.permissionMode || 'default'
diff --git a/src/server/services/sessionService.ts b/src/server/services/sessionService.ts
index 64b55095..19052a1a 100644
--- a/src/server/services/sessionService.ts
+++ b/src/server/services/sessionService.ts
@@ -803,12 +803,11 @@ export class SessionService {
    * Find the .jsonl file for a given session ID.
    * Searches across all project directories since sessions may belong to any project.
    */
-  async findSessionFile(
+  private async findSessionFiles(
     sessionId: string
-  ): Promise<{ filePath: string; projectDir: string } | null> {
-    // Validate sessionId format to prevent path traversal
+  ): Promise<Array<{ filePath: string; projectDir: string }>> {
     if (!this.isValidSessionId(sessionId)) {
-      return null
+      return []
     }
 
     const projectsDir = this.getProjectsDir()
@@ -817,20 +816,27 @@ export class SessionService {
     try {
       projectDirs = await fs.readdir(projectsDir)
     } catch {
-      return null
+      return []
     }
 
+    const matches: Array<{ filePath: string; projectDir: string }> = []
     for (const dir of projectDirs) {
       const filePath = path.join(projectsDir, dir, `${sessionId}.jsonl`)
       try {
         await fs.access(filePath)
-        return { filePath, projectDir: dir }
+        matches.push({ filePath, projectDir: dir })
       } catch {
         continue
       }
     }
 
-    return null
+    return matches
+  }
+
+  async findSessionFile(
+    sessionId: string
+  ): Promise<{ filePath: string; projectDir: string } | null> {
+    return (await this.findSessionFiles(sessionId))[0] ?? null
   }
 
   private isValidSessionId(id: string): boolean {
@@ -1460,12 +1466,25 @@ export class SessionService {
       repository?: PreparedSessionWorkspace['repository']
     }
   ): Promise<void> {
-    const found = await this.findSessionFile(sessionId)
-    if (!found) return
+    const matches = await this.findSessionFiles(sessionId)
+    if (matches.length === 0) return
 
-    const entries = await this.readJsonlFile(found.filePath)
-    const repository = metadata.repository ?? this.resolveRepositoryFromEntries(entries)
-    await this.appendJsonlEntry(found.filePath, {
+    let repository = metadata.repository
+    if (!repository) {
+      for (const match of matches) {
+        const candidate = this.resolveRepositoryFromEntries(await this.readJsonlFile(match.filePath))
+        if (candidate) {
+          repository = candidate
+          break
+        }
+      }
+    }
+
+    const targetProjectDir = this.sanitizePath(metadata.workDir)
+    const targetFilePath = path.join(this.getProjectsDir(), targetProjectDir, `${sessionId}.jsonl`)
+    await fs.mkdir(path.dirname(targetFilePath), { recursive: true })
+
+    await this.appendJsonlEntry(targetFilePath, {
       type: 'session-meta',
       isMeta: true,
       workDir: metadata.workDir,
@@ -1474,7 +1493,7 @@ export class SessionService {
     })
 
     if (metadata.customTitle) {
-      await this.appendJsonlEntry(found.filePath, {
+      await this.appendJsonlEntry(targetFilePath, {
         type: 'custom-title',
         customTitle: metadata.customTitle,
         timestamp: new Date().toISOString(),
diff --git a/src/server/ws/handler.ts b/src/server/ws/handler.ts
index e30a9135..247f9cb3 100644
--- a/src/server/ws/handler.ts
+++ b/src/server/ws/handler.ts
@@ -775,6 +775,7 @@ function markPrewarmed(sessionId: string) {
 function cacheSessionInitMetadata(sessionId: string, cliMsg: any) {
   if (cliMsg?.type !== 'system' || cliMsg.subtype !== 'init') return
   if (typeof cliMsg.cwd === 'string' && cliMsg.cwd.trim()) {
+    conversationService.updateSessionWorkDir(sessionId, cliMsg.cwd)
     void (async () => {
       await sessionService.appendSessionMetadata(sessionId, {
         workDir: cliMsg.cwd,