[BUG] Opening a prior Cowork session silently overwrites global instructions with the version from that session

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?

Labels: bug, area:cowork, area:settings

[BUG] Opening a prior Cowork session silently overwrites global instructions with the version from that session

Warning: This bug corrupts a setting that governs all sessions. The overwrite happens silently — there is no warning, confirmation prompt, or visible indicator that global instructions have changed.

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Preflight checklist

• I have searched existing issues and this has not been reported in this form
• This is a single bug report
• I am using the latest version of Claude Desktop

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What's wrong

When global instructions are updated in Settings > Cowork > Global instructions and a prior Cowork session is subsequently opened, the global instructions are silently reverted to whichever version was active when that session was last used or started.

The overwrite is permanent and silent — there is no warning, diff, or confirmation. The user has no way of knowing their current global instructions have been replaced unless they manually navigate back to settings to verify.
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Expected behaviour

Global instructions represent a user-level setting that should persist independently of any individual session. Opening a prior session should never modify global instructions. If there is a version mismatch between the session context and current global instructions, the user should be notified — not silently overwritten.

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Actual behaviour

Opening a prior session reverts global instructions to the version stored with that session. This occurs silently with no user notification, confirmation prompt, or visible indicator. The issue is 100% reproducible and was confirmed through repeated testing over an extended period.

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Impact

• All subsequent Cowork tasks run with stale or incorrect global instructions without the user's knowledge
• Updates to global instructions (role context, preferences, output format) are lost silently
• No reliable way to maintain current global instructions while keeping access to prior sessions

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Workaround applied

All prior sessions were retired. A session was relabelled DO NOT USE ANYTHING OLDER THAN THIS to mark the cutoff point. Transitioned entirely to the Projects approach to avoid re-triggering the issue. This workaround results in permanent loss of prior session context.

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Environment

• Platform: macOS
• Claude Desktop: latest version
• Plan: Max

What Should Happen?

Global instructions represent a user-level setting that should persist independently of any individual session. Opening a prior session should never modify global instructions. If there is a version mismatch between the session context and current global instructions, the user should be notified — not silently overwritten.

Error Messages/Logs

N/A

Steps to Reproduce

1. Open Claude Desktop and navigate to Settings > Cowork > Global instructions
2. Update global instructions with new content. Save.
3. Confirm the new instructions are saved by revisiting the settings field.
4. Open any prior Cowork session (one started before the update was made).
5. Navigate back to Settings > Cowork > Global instructions.
6. Observe that global instructions have reverted to the version that was active when that prior session was last used.

Claude Model

Not sure / Multiple models

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

latest

Platform

Other

Operating System

macOS

Terminal/Shell

Other

Additional Information

_No response_