I usually call and give them my situation and ask if I can bring it by for them to look at if the problem warranty acceptable. My dealership is pretty good about honoring warranties with a modded car. But your case sounds like something they might deny since it'd be someone else's fault. They almost denyed me about that black trim infront of the wheelwell being ripped off, but I think he reconized me from before and did it under good faith.
"We live for a good time, not a long time."
RIP Colin McRae