Codex App: saving Settings → Personalization → Custom instructions silently replaces the entire `~/.codex/AGENTS.md` (existing global instructions lost)

What version of the Codex App are you using (From "About Codex" dialog)?

26.814.41407 (ChatGPT/Codex merged desktop app for macOS; Codex CLI 0.147.0)

What subscription do you have?

Pro

What platform is your computer?

Darwin 25.4.0 arm64 arm (macOS 26.4.1)

What issue are you seeing?

~/.codex/AGENTS.md is used as the global instruction file for Codex. In the merged ChatGPT/Codex desktop app, Settings → Personalization → Custom instructions reads from and writes to this same file (see #35202, #33792, #38859).

When I typed a short instruction into that field (3 short lines about reply tone, intended to also apply to voice chat) and saved, the app overwrote the whole ~/.codex/AGENTS.md with just those 3 lines. My existing global instructions (~4,000 characters of operational rules built up over weeks — tool priorities, browser-use authorization, timezone handling, handover rules, etc.) were deleted with no warning, no confirmation, and no backup.

Because nothing in the UI says "this field IS ~/.codex/AGENTS.md", I did not notice for about a week. During that time Codex behaved noticeably worse (ignored rules it used to follow), and I only found the cause by diffing the AGENTS.md text embedded in old session rollouts under ~/.codex/sessions/ against the current file.

Timeline (from rollout files; JST):

• Before saving — rollouts still embed the full ~4,000-char global AGENTS.md
• Custom instructions saved in the app
• A few minutes later — new rollouts embed only the 3 new lines. No Codex/CLI session wrote the file in that window.

What steps can reproduce the bug?

1. Put any multi-section content in ~/.codex/AGENTS.md (e.g. 50+ lines of global rules).
2. Open the Codex/ChatGPT desktop app → Settings → Personalization → Custom instructions.
3. The field shows the current AGENTS.md content. Replace it with (or type) a short instruction and save.
4. cat ~/.codex/AGENTS.md → the file now contains only what was in the field. Previous content is gone; no .bak, no prompt.

(No thread/session ID applies — the write came from the settings UI, not from a Codex thread.)

What is the expected behavior?

Any of the following would have prevented the data loss:

• The Personalization field should clearly state that it edits ~/.codex/AGENTS.md (full path), and show a confirmation when the save would remove existing content.
• Keep a backup (e.g. AGENTS.md.bak-<timestamp>) before overwriting a file that was modified outside the app.
• Better: keep ChatGPT "custom instructions" separate from the Codex global AGENTS.md (as requested in #35202), or append/merge into a clearly delimited block instead of replacing the file.

Additional information

• Related: #35202 (custom instructions written to ~/.codex/AGENTS.md and shared across Chat/Codex/Work), #33792, #38859 (Personalization shows Codex global instructions), #37950 (voice sessions don't receive AGENTS.md — which is why I was adding a voice-related instruction there in the first place).
• I recovered the content from the # AGENTS.md instructions block embedded in older rollout .jsonl files; that may be useful to others hit by this.