[BUG] User text messages in continuation sessions are not persisted to the JSONL transcript file

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?

User text messages in continuation sessions are not persisted to the JSONL transcript file
Only tool_result entries are logged, human text entries are dropped
This means if the terminal scrolls or refreshes, submitted user messages are unrecoverable

What Should Happen?

If submitted in tan then should be stored so any reset or stoppage does not lose the inputs

Error Messages/Logs

Steps to Reproduce

Here's what to include in the bug report:

Steps to Reproduce:

1. Start a Claude Code session and have a long conversation until context compaction/continuation occurs
2. Continue the session (continuation summary loads)
3. Send several messages — they appear in tan (submitted) in the terminal
4. While Claude is mid-response (running tools, fetching URLs, etc.), type and submit additional messages
5. Press Escape or type "stop" to interrupt Claude's response
6. Scroll up — the previously submitted tan messages are gone from the terminal display
7. Check the JSONL transcript file — user text messages from the continuation session are missing; only tool_result entries are logged

Expected Behavior:

• All submitted user messages should persist in the terminal scroll history
• All submitted user messages should be written to the JSONL transcript file
• Interrupting Claude's response should never affect previously submitted user messages

Actual Behavior:

• User text messages in continuation sessions are not written to the JSONL transcript
• Only tool_result (automatic system) entries are persisted
• Submitted messages disappear from the terminal and are unrecoverable

Environment:

• Windows (win32)
• Session ID: 854d3bba-3d7e-47d2-b56a-fc8ea6931b11
• JSONL file: 6159 lines, 28MB — zero user text entries in the continuation portion (last ~3000 lines), despite multiple messages being sent and displayed

Impact: User loses work — typed comments, URLs, widget names, notes — with no way to recover.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

v2.1.34

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_