A screenshot would help, but just guessing based on the description she’s seeing the layouts from Paratext 8.0 which we don’t allow to be deleted via PT9.
Unfortunately, she’ll have to delete them manually from the _WindowCollections directory (old ones will have a .ptwc extension instead of a .ptwc2 extension). Note that deleting them will be permanent, so it might be best to move them somewhere else, make sure that solves the problem, then move any she needs back.