If you imported the existing projects from database, it's ok that Skipper is now trying to create the migration.
It's because Skipper doesn't know whether you need to create it or not.
But you can select initial imported migration to not be exported to database by managing migrations and select "Enable/disable revision"
Thanks for this feedback. We will improve import process so Skipper will ask you whether to mark migration with existing tables as non-exportable.