Session lost after helper tool update — transcript intact but unrecoverable

Bug Description

A long-running Claude Code session (nearly 3 months, 1.2 GB transcript, 118,156 lines) became permanently unrecoverable after the Claude desktop app prompted to install a helper tool update. The session process died during the update prompt, and the app lost the session from its internal index. The transcript file and all associated data remain fully intact on disk, but no recovery mechanism exists.

Steps to Reproduce

1. Have a long-running Claude Code session active in the desktop app
2. Claude prompts to install a helper tool update (macOS authorization dialog)
3. If the user's account lacks admin privileges at that moment, the update fails
4. The session process dies
5. The session disappears from the sidebar and /resume picker

What Happened

• Session vanished from the desktop app sidebar
• /resume does not list the session (even with search by title or ID)
• claude --resume <session-id> from CLI shows fresh setup wizard instead of resuming
• get_session via MCP returns "Session not found"
• list_sessions (including archived) does not include the session

What's Still on Disk (intact)

• Transcript: ~/.claude/projects/<project>/68cc8f0f-c179-4b57-9a3a-937af2c57ad1.jsonl — 1.2 GB, 118,156 lines
• Session directory: 68cc8f0f-c179-4b57-9a3a-937af2c57ad1/ with 4,011 subagents, 46 tool-results, and workflows
• All data is intact and readable — user messages, assistant responses, tool outputs all present

Session Details

• Session ID: 68cc8f0f-c179-4b57-9a3a-937af2c57ad1
• Auto-title: "Assess lawsuit strategy and research defenses"
• Started: June 18, 2026
• Last active: September 11, 2026 (the morning it was lost)
• Duration: ~85 days of continuous use
• Size: 1.2 GB transcript, 4,011 subagents
• Platform: macOS Darwin 23.6.0 (Apple Silicon)
• Claude Code version at creation: 2.1.177
• Entrypoint: claude-desktop

Expected Behavior

1. The app should not lose session registration when the helper tool update fails
2. /resume should be able to rediscover sessions from intact JSONL transcript files on disk
3. There should be a recovery mechanism (e.g., claude --recover <session-id>) for orphaned sessions whose transcripts are intact

Impact

This session contained nearly 3 months of complex legal research and document preparation work. All the files produced are intact, but the conversational context, accumulated understanding, and session state are inaccessible. The user relied on being able to continue this session.

Environment

• macOS 14.x (Darwin 23.6.0)
• Claude Desktop App
• Claude Code