Hi! As stated in Cannot enable passkey for custom database it is not possible to enable passkeys on a database connection that was migrated before.
Since the original issue is closed with a very unsatisfying answer I wanted to open this topic to make sure there will be a solution for this in future. I think its not a applicable solution to block out users from using passkeys that have used migrations before.
The thing thats most confusing is that I store no data on any custom database anymore and still cannot switch off the custom database flag. This is really a problem for us.