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Codex Desktop fails to start with migration 1 was previously applied but has been modified #23824

Closed as duplicate
Closed as duplicate
Codex Desktop fails to start with migration 1 was previously applied but has been modified#23824
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appIssues related to the Codex desktop appbugSomething isn't workingwindows-osIssues related to Codex on Windows systems

Description

@miku-lilac
miku-lilac
opened on May 21, 2026

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

26.520.11634

What subscription do you have?

Pro

What platform is your computer?

Microsoft Windows NT 10.0.26200.0 x64

What issue are you seeing?

Codex Desktop fails to launch with the following error:

Codex cannot access its local database.

Database path:
/mnt/c/Users/<user>/.codex/state_5.sqlite

Most recent error:
Error: failed to initialize sqlite state db at
/mnt/c/Users/<user>/.codex/state_5.sqlite:
failed to initialize state runtime at
/mnt/c/Users/<user>/.codex:
migration 1 was previously applied but has been modified

What steps can reproduce the bug?

  1. Install Codex Desktop on Windows
  2. Use WSL integration
  3. Launch Codex

What is the expected behavior?

No response

Additional information

No response

Activity

  1. miku-lilac
    added
    appIssues related to the Codex desktop app
    on May 21, 2026
  2. github-actions
    added
    bugSomething isn't working
    windows-osIssues related to Codex on Windows systems
    on May 21, 2026

  3. github-actions commented on May 21, 2026

    @github-actions
    github-actionsbot
    on May 21, 2026 – with GitHub Actions
    Contributor

    Potential duplicates detected. Please review them and close your issue if it is a duplicate.

    Powered by Codex Action

  4. miku-lilac
    closed this as a duplicateof Codex Windows App reported an error after upgrading: Codex cannot access its local database #23780 on May 21, 2026

  5. xdifu commented on May 21, 2026

    @xdifu
    xdifu
    on May 21, 2026

    For anyone landing here from search: this matches the CRLF/LF SQLx checksum issue tracked in #23777 / #23787. The WSL/Linux backend rejects a Windows-created state_5.sqlite because the stored _sqlx_migrations checksum was computed from different line-ending bytes.

    I published a non-destructive recovery tool here: https://github.com/xdifu/codex-repair

    Windows PowerShell / Windows Terminal:

    git clone https://github.com/xdifu/codex-repair.git
cd codex-repair
python codex-repair.py fix --apply

    If you run it from WSL bash to repair Windows Codex Desktop data, pass --codex-home "/mnt/c/Users/<WindowsUser>/.codex" so it does not target WSL's own ~/.codex.

    It backs up state_5.sqlite / logs_2.sqlite, schema-verifies before any checksum rewrite, and keeps ~/.codex/sessions/*.jsonl read-only.

  6. Nerexis commented on May 21, 2026

    @Nerexis
    Nerexis
    on May 21, 2026

    @xdifu Your fix has worked fine for me. Thank you.

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