If it is cat-back exhaust and that exhaust was carb approved i dont think they could deny anything. Anything after the cats just has to do with noise and has nothing to do with performance or the computer etc....having carb approval and a warranty on the installed part can help too...that way if honda says it caused a problem you can go to installer and let them fight with honda over whos problem it is to fix....they both cant be right.
Just my .02
B