For sure the warranty on the factory IC you are replacing will be void. But the rest of your car’s warranty should still be intact. Putting in an IC wouldn’t necessarily be related to, let’s say the brake components or your electrical components. So if you get the midpipe rattle, as most do. They most likely won’t come back and say “no, we can’t replace your midpipes because you swapped out your IC” Each dealership will be different though.