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You probably need to raise a support ticket for this. I've just been on the phone for an hour with support, and they have a workflow which they ask you to run in addition to various cleanup on the MongoDB.
Hopefully you have more luck than we did - couldn't get to a persistent fix. I'll be going back to an old backup. Thankfully this is just our test environment.
Hello @Peter_K and @Stephan_Braun, what you are seeing is a hidden feature for moving Workflows out of a Private studio so that they do not get orphaned. Please see this Knowledge Base Article that explains what is happening.