Your warranty will still stand ... unless the modification you installed is a direct cause of the problem you're having. Like ... if you put a Cold-Air Intake on your engine and that intake sucks some water into the cylinders and you bend a handful of rods and lose compression in some of the cylinders then, sorry you're out of luck. They don't have to fix it for you. If you, however, install a cat-back exhaust and suddenly the shift linkage snaps then you can bring your car in and they have to fix your transmission under warranty.

They can only cancel your warranty if an aftermarket part caused the failure or damage. And at that, they can only cancel the warranty on the component that the aftermarket part damaged. If you throw on a supercharger and your engine blows up and you can still take it in to get your blown stock speaker fixed. They just won't fix your engine.
And, the burden of proof of failure is on them. They have to show that the aftermarket component was what caused the failure, that it wasn't a fault that would have occured regardless of the aftermarket part.