When a Branch is deleted from the Git repository before the expire time set on the Automatically Manage Branches menu and the Branch Plan is still run by Bamboo but an error is given on the error logs:

Plan 'TESTPLAN20' could not be started. Exception: com.atlassian.bamboo.repository.InvalidRepositoryException: Cannot determine head revision of 'https://github.com/example/example.git' on branch 'example/branch'. Branch has probably been removed.

Plan 'TESTPLAN20' detected that the repository is invalid. The plan will be disabled.

That branch is then disabled but remains on the branch list indefinitely. Bamboo should remove that Branch from the list as the branch does no longer exists.