Session transcript silently lost when reopening session in desktop app — 57 turns unrecoverable

Bug description

A long-running session (57 completed turns, created 2026-03-24, last active 2026-05-12) opened blank in the Claude Desktop app. All prior conversation history was silently lost with no warning or recovery path.

What happened

1. Opened an existing session titled "Create user research participant recruitment strategy" in the Claude Desktop app
2. The chat window displayed blank — no prior messages visible
3. The session contained extensive work over ~7 weeks: user research discussion guides, transcript analysis, recruitment strategy, and accumulated context
4. All 57 turns of conversational context are permanently lost

Technical details

• Session metadata file (~/Library/Application Support/Claude/claude-code-sessions/.../local_[sessionId].json) is intact — correct title, 57 completedTurns, all tool permissions preserved
• CLI transcript file (~/.claude/projects/.../[cliSessionId].jsonl) contains only messages from after the blank reopening — prior content appears to have been overwritten when the session was reopened
• No backup, versioning, or .bak copy of the transcript file exists on disk
• The metadata cliSessionId correctly points to the JSONL file, but the JSONL file no longer contains the original conversation

Expected behaviour

• Session should reopen with full conversation history intact
• If transcript data is at risk of being overwritten, there should be a backup mechanism or at minimum a warning
• Transcript files should not be silently replaced when a session is reopened

Impact

This session contained substantial non-recoverable work — research discussion guides, analysis of user interview transcripts, a recruitment strategy, and weeks of accumulated project context. The output files exist but the conversational context (reasoning, decisions, iterative refinements) is permanently lost.

Environment

• OS: macOS 26.4.1 (Darwin 25.4.0)
• Claude Code: 2.1.80
• App: Claude Desktop (claude-code-sessions integration)
• Model: claude-opus-4-6