Mass compile will update all your vi's in the refered directories to LV 6.0.2. This is good if you want that, but if you want to mantain some vi's in a previous release form to open them with it, you must avoid including them. Hope this helps
Each of the VIs that you open that are in a previous version will ask if you want to save them in teh new version when you close anyway. I think that not updating and just doing them "as you use them" is the better way to go (for saving time).
On the other hand, I told my computer to mass compile and then went home for the evening. Pick your time.