[BUG] Sidebar groups disappeared and can't be restored, when I create a new session they all go to a single folder

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?

Two sidebar groups in Claude Desktop — "milestone-iterations" and "ai-guidance-beta" — disappeared entirely from the left sidebar. Sessions that had originally been in those groups are now lumped into a different group ("ai-copilot-concept-testing"). New chats also default to that wrong group with no way to change which group is the default. Right-clicking a session and selecting "Move to group" only offers "Create new group" — there's no dropdown of existing groups to pick from. Even after fully quitting (Cmd+Q) and relaunching the app, the missing sections never reappear.

What Should Happen?

1. What should happen

Sidebar groups should be re-derived from each session's working-directory metadata on app launch, so editing the underlying session files reflects in the UI after restart.
A group that becomes empty shouldn't be permanently removed — or if it must be, there should be a UI way to restore/recreate it explicitly.
"Move to group" should let me pick from a list of existing groups, not only offer "Create new group."
New chats should respect a configurable default group, or at minimum let me pick which group a new chat goes into at creation time.

Error Messages/Logs

Error message logs
No error messages in the Claude Desktop UI — the app fails silently with no notification or warning. Sessions just appear in the wrong place and groups just vanish.
Claude Code debug log (~/.claude/debug/<session-id>.txt) shows 0 ERRORs and 0 WARNs — Claude Code itself is healthy. The problem is in the Desktop app, not the agent runtime.
No relevant entries in Console.app or system logs for the Claude process during the failure window.
I was unable to locate any config file or database table that explicitly records group membership — it appears to be stored in the app's IndexedDB (~/Library/Application Support/Claude/IndexedDB/), which is opaque from outside the app.

Steps to Reproduce

Approximate reproduction (this happened over a long session, but the pattern is clear):

Start with multiple sidebar groups, each containing some sessions
Modify the cwd and/or originCwd fields of session JSON files at ~/Library/Application Support/Claude/claude-code-sessions/<workspace>/<project>/local_*.json — moving sessions out of one group and into another by changing the path values
Cmd+Q and relaunch Claude Desktop
First time: the destination group is created from the new cwds and the sessions appear there ✓
Subsequently, when sessions are moved out of an existing group such that the group becomes empty, that group disappears from the sidebar
Trying to put sessions back into the disappeared group by reverting their cwd/originCwd — the group does not reappear after relaunch, even though sessions have correct paths on disk
Restoring the entire session JSON folder from a pre-edit backup also does not restore the missing groups — the Desktop app's internal cache treats them as permanently deleted

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude Code: 2.1.121

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_