[BUG] Desktop app session history missing + references nonexistent session ID, breaking message processing (Windows)

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 related but distinct issues:

Two related but distinct issues on Claude Code for Windows.

1. Display bug: Session history does not appear in the Claude desktop app's session list, or in the CLI's in-session /resume picker. Confirmed via filesystem that .jsonl session files are intact and non-empty (ranging 17KB–7MB) across multiple project folders under ~/.claude/projects/. Running claude --resume <session-id> directly from the terminal with a known session ID works correctly and restores the session, confirming this is a display/discovery bug, not data loss. A full quit and restart of the desktop app did not resolve it. This matches the pattern reported in #27752 and #57203.

1. Session desync causing message failures: After running /doctor inside the desktop app, sending a new message failed with:

No conversation found with session ID: 015f4114-e64b-4091-9daa-ca8c81cdb876

A filesystem-wide search confirms no .jsonl file with this ID exists anywhere under ~/.claude/projects/. The app appears to reference an internal session ID that was never persisted to disk. This broke the ability to send any new message in the app.

What Should Happen?

Every session with an intact .jsonl file under ~/.claude/projects/ should appear in both the desktop app's session list and the CLI's /resume picker, without requiring the user to know the session ID in advance.
Running /doctor should not alter or corrupt the active session context. If it does start a new session, that session should be properly created and persisted, not just referenced.
Sending a message should never fail because of a reference to a nonexistent session ID. At minimum, the app should recover the last known-good session or start a genuinely new one, rather than getting stuck.

Error Messages/Logs

Steps to Reproduce

Steps to reproduce (issue 1):

Have multiple existing sessions across several project directories.
Open the desktop app, or run claude --resume interactively in the CLI.
Session list/picker shows empty or missing sessions.
Confirm via filesystem (Get-ChildItem -Recurse -Filter *.jsonl under ~/.claude/projects/) that files exist with real content.
Confirm via claude --resume <session-id> (direct, non-interactive) that the session resumes correctly.

Steps to reproduce (issue 2):

Open Claude Code desktop app with existing session history.
Run /doctor in-session.
Send a new message.
App returns "Claude couldn't process that message" with a session-not-found error.
Confirm via filesystem search that the referenced session ID does not exist anywhere on disk.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.228

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_