Well I suppose you could make the xf instance copy, delete the stuff you don't want from copy 2, then import that copy into a clean install without retaining content IDs and you should achieve pretty close to what I think you are looking to do.
Haven't thought about it before 2 seconds ago but without thinking much (I am good at that) I would guess that it will scrub as much of the residue away that is possible without re-entering all of your content manually.