Always put back your stock part if you can whenever you are going in for warranty work. I have seen countless dumbasses on a variety of boards bringing in their cars with the mods and having their warranty denied because of these mods. Tenchically, a dealership has to prove that the mod cause the failure but most dont gave a dam and the first thing they see that is modified, they will denied you warranty.

Some dealership are cool with modifciations, some are not. But my advice is always put back your stock part if you can, even if it's a hassle.