I've noticed the Ghosting: x% bar stays up if I don't let it finish (a la, this issue).

Unless your contraption is really complex and takes ages to finish ghosting, I usually just take out Adv. Dupe again, let it ghost, then select something else.

Something that might be useful could be adv. duping say a single prop, then saving that. That way if you get stuck with the ghosting box, you can load a super-simple dupe that takes no time to finish ghosting.