@Geert: I found the xml of the former profile, imported it, unchecked the old stereotype, and re-imported the newest profile. Seems to be solved now. Sure, it is an omission in UI specification. But I guess, not many users are burdened by it. And there is a workaround, if you have good version control.
@qwerty: Using Dbeaver I had a look at t_xref (there is no t_ref) and found the used stereotype by 'Description like "*<the old stereotype>"'. Made a copy of the model and deleted those line. Works great as well. If you want to rename a stereotype that is used often, this seems to be a good method. Also the omission of renaming a stereotype looks like a point for improvement.
@Modesto: EA16.0 1605