If get a tune that has offroad xpipe as one of the mods and have to put the catted pipe back on for emission reasons... would the tune be ineffective and be best to be stock or would the xpipe not make that big a difference in how they program the tune? Completely oblivious on this issue

 

If you're deleting the cats, and then putting them back on, I'd return to stock tune or a tune prep'd for cats on.