[BUG] Desktop app shows "Bypass Permissions mode isn't enabled" notification on every new session despite defaultMode: bypassPermissions in settings.json

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?

Every time a new session is started in the Claude Code desktop app (macOS), the following notification appears immediately after the first message is sent:

"Bypass Permissions mode isn't enabled. The session started in Accept Edits — enable Bypass Permissions in Settings to use it."

Steps to reproduce:

1. Open Claude Code desktop app (macOS)
2. 2. Start a new session — the bottom toolbar correctly shows "Bypass permissions" in yellow
3. 3. Type and send any message
4. 4. The notification appears, claiming the session started in Accept Edits mode

Settings configuration (already correctly set):
~/.claude/settings.json:

{
  "skipDangerousModePermissionPrompt": true,
  "permissions": {
    "defaultMode": "bypassPermissions"
  }
}

Observation: The main session appears to actually work in Bypass Permissions mode (tool calls proceed without individual permission prompts), but the notification fires anyway. The UI bottom bar shows "Bypass permissions" correctly before the first message, yet the notification appears after sending the first message. The notification seems to be a false positive — possibly triggered by a sub-process or background agent starting in Accept Edits mode while the main session remains in Bypass Permissions mode.

This has been happening persistently across many sessions and after multiple attempts to reconfigure settings.

What Should Happen?

No notification should appear when defaultMode: bypassPermissions is set in ~/.claude/settings.json and the UI bottom bar already shows "Bypass permissions". The session should start silently in Bypass Permissions mode as configured.

Error Messages/Logs

Notification text: "Bypass Permissions mode isn't enabled. The session started in Accept Edits — enable Bypass Permissions in Settings to use it."

App: Claude Code desktop app (macOS)
Version: 1.8555.2 (latest)
OS: macOS Darwin 25.3.0

Steps to Reproduce

1. Open Claude Code desktop app on macOS
2. 2. Start a new session (working directory: any)
3. 3. Confirm the bottom toolbar shows "Bypass permissions" in yellow text
4. 4. Type any message and send it
5. 5. Observe: notification "Bypass Permissions mode isn't enabled. The session started in Accept Edits — enable Bypass Permissions in Settings to use it." appears

Note: ~/.claude/settings.json has "defaultMode": "bypassPermissions" and "skipDangerousModePermissionPrompt": true already set. The notification appears on every single new session.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.0.8555 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_