[BUG] alwaysThinkingEnabled setting not recreated after being deleted via /config toggle

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?

Description:
When toggling extended thinking off via /config, the alwaysThinkingEnabled key is deleted from settings.json instead of being set to
false. Subsequently, when trying to enable thinking again via /config, the setting fails to be recreated, leaving the user unable to
enable thinking mode through the UI.

Actual Behavior:

• Toggle off deletes the key
• Toggle on fails to recreate the key when it doesn't exist

Workaround:
Manually add "alwaysThinkingEnabled": true to ~/.claude/settings.json

Environment:

• Claude Code version: 2.1.1
• OS: macOS (Darwin 25.2.0)

What Should Happen?

• Option A: Toggle off should set alwaysThinkingEnabled: false instead of deleting the key
• Option B: Toggle on should create the key if it doesn't exist

Error Messages/Logs

Steps to Reproduce

1. Enable extended thinking via /config → alwaysThinkingEnabled: true is added to ~/.claude/settings.json
2. Disable extended thinking via /config → the alwaysThinkingEnabled key is completely removed from settings.json
3. Try to enable extended thinking again via /config → the key is not recreated, thinking remains disabled

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.0.74

Claude Code Version

2.1.1

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

_No response_