It would be nice to have some sort of notification on the admin side that the course already has content. Not sure if something could be added in the sync history to notify something isn't right.
Not sure how this would work from the teacher's end because they may not realize it is associated with a blueprint. Our empty course shells and enrollments are up before we sync blueprints. Some of the new faculty sometimes just start doing things not understanding how the blueprint works and jump on things before their course leads are ready.