Session .jsonl transcript silently deleted while session folder remains — deletion pattern doesn't match simple age-based retention

Summary

Session transcripts (~/.claude/projects/<project>/<uuid>.jsonl) disappear from disk while the session's auxiliary directory (~/.claude/projects/<project>/<uuid>/tool-results/, which caches SessionStart hook output) remains intact. This affects real, substantial interactive conversations — not just short/automated sessions — and the temporal pattern does not match a simple age-based retention sweep.

Environment

• Claude Code CLI: 2.1.272 (native binary, /joao/.local/bin/claude)
• Claude Code VS Code extension (code-server): 2.1.276
• OS: Ubuntu 24.04.4 LTS, self-hosted VPS
• cleanupPeriodDays is not set in either ~/.claude/settings.json or ~/.claude.json
• fileCheckpointingEnabled: true (used only for /rewind, per docs — confirmed not related)

Observed behavior (measured directly on disk)

Across multiple project directories under ~/.claude/projects/, most session folders (identified by a valid UUID) no longer have their companion .jsonl transcript, while the folder itself — and its tool-results/ cache from the SessionStart hook — still exists:

I cross-referenced this against a separate local database (a memory plugin that records content_session_id + started_at + first user prompt for every session that ever ran) to distinguish two very different situations:

1. Automated/non-interactive sessions (skill runs triggered by cron, autonomous sub-agent task executions, git-worktree sessions) — most of the missing-transcript count falls here (e.g. 163 of 218 in one project). This may be expected/acceptable.
2. Real interactive human conversations with substantial content — a smaller but recurring subset. Example: a session that ran for ~8 minutes, produced 11 distinct pieces of work (document analysis, calendar events created, files edited), and both its .jsonl and its folder are now completely gone — no trace at all on disk, not even the tool-results/ cache. This is a different, more severe symptom than "folder survives, only .jsonl is missing."

What I ruled out

• No cron/systemd timer or user script touches ~/.claude/projects/ on this machine (verified: crontab, systemd timers, grep -r across all local scripts).
• Not the documented /compact behavior: found a live isCompactSummary: true entry inside a transcript that survived — it uses the same sessionId, appended within the same .jsonl file. Compaction does not create a new file or delete the old one.
• Not a VM reboot: last reboot shows uptime since 2026-08-20, no reboot around the dates the deletions occurred.
• Not a simple age-based sweep relative to "today": in one project, a session from yesterday has already lost its .jsonl, while a session from 29 days ago still has its .jsonl intact. This directly contradicts "delete anything older than N days, checked against today's date."

What's unclear from the docs

settings.json reference documents cleanupPeriodDays only as "control how many days Claude Code retains transcripts before automatic deletion" — it doesn't state the default value when the key is absent, nor how to disable the sweep entirely, nor whether the sweep trigger is time-based (a periodic check) or event-based (e.g. only evaluated when a new session starts in that same project directory — which would better explain why deletions cluster in bursts rather than following a smooth daily pattern).

Question

1. What is the actual default retention period when cleanupPeriodDays is unset?
2. Is there a way to fully disable transcript deletion (not just increase the number of days)?
3. Why would a session's .jsonl be deleted while its tool-results/ folder (or, in the more severe case, the entire session folder) is not touched by the same sweep — and in the severe case, why would a real, substantial, non-trivial interactive session be eligible for deletion at all after only ~6 weeks?

Happy to provide more specific session IDs/timestamps privately if useful for debugging — omitted here since this repo is public and some of that data touches personal projects.

Start by checking ~/.claude/settings.json and ~/.claude.json, then reproduce transcript cleanup while comparing .jsonl files, session folders, and tool-results/ directories under ~/.claude/projects/. Determine the unset cleanupPeriodDays behavior, whether deletion can be disabled, and why transcripts or complete session folders are selected; done means documenting or fixing each observed case.