[BUG] Cowork sidebar Pinned/Projects list incomplete — internal .claude/projects/ index out of sync with actual project source folders

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Environment:

OS: Windows
Claude Desktop version: 1.28929.0 (d1a6bc)
Mode: Cowork

What's Wrong?

The Cowork sidebar's Pinned/Projects list no longer shows most of my existing projects. Restarting the app does not fix it. However, the underlying project data is fully intact on disk — this is an indexing/sync problem, not data loss.

Evidence:

Documents\Claude\Projects\ (the actual project source folders) contains 14 complete project folders, untouched and fully intact:
00_AI_learning, 01_ISO_9001_2026, 02_ESG, 03_EPD_RA, 04_公司雜務, 11_Pokemon Sleep, 12_PC game, 13_Tennis, 14_Travel, 15_Linux, 16_PC, 17_記帳app開發, 19_科學知識, 21_Stock_Market, 91_Rapid_Test_(Maggie)
C:\Users\<user>\.claude\projects\ (the internal index Cowork appears to use for the sidebar) only contains 11 entries, and does not match the full list above — folders like 04_公司雜務, 12_PC game, 14_Travel, 15_Linux, and 91_Rapid_Test_(Maggie) are missing from this index entirely, even though their source folders exist.
C:\Users\<user>\.claude\sessions\ contains only a single file (e.g. 3780.json) — all other session records appear to have been dropped from this index as well.
No user action was taken (no manual deletion, no reinstall). The app was simply restarted.
Restarting Claude Desktop does not repopulate the sidebar or the index.

What Should Happen?

Expected behavior: The Cowork sidebar should reflect all projects present in Documents\Claude\Projects\, and .claude/projects/ + .claude/sessions/ should stay in sync with that source directory.

Actual behavior: Sidebar shows an incomplete/empty Pinned list; internal index folders are missing entries for several projects that still exist in full on disk.

Impact: No data loss confirmed so far (source folders intact), but loss of session history/context and inability to access projects via the normal UI.

Error Messages/Logs

Steps to Reproduce

1. Use Claude Desktop (Cowork mode) normally over multiple sessions/days, creating and working in multiple projects under Documents\Claude\Projects\ (in my case: 14 project folders accumulated over ~1 month).
2. Restart Claude Desktop app.
3. Open the Cowork sidebar and check the Pinned/Projects list.
4. Observe: the sidebar shows an incomplete list — several projects that exist in Documents\Claude\Projects\ do not appear.
5. Check

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Unknown / not tracked.

Claude Code Version

1.28929.0 (d1a6bc)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Other

Additional Information

<img width="999" height="1051" alt="Image" src="https://github.com/user-attachments/assets/1e9c98a5-94b7-4a93-a672-cb4966a297a3" />

<img width="704" height="744" alt="Image" src="https://github.com/user-attachments/assets/d670f06b-3a47-493b-8b96-70b8d7023e13" />