Legally, a vehicle manufacturer cannot void the warranty on a vehicle due to an aftermarket part unless they can prove that the aftermarket part caused or contributed to the failure in the vehicle (per the Magnuson Moss Warranty Act (15 U.S.C. 2302(C)) . For best results, consider working with performance-oriented dealerships with a proven history of working with customers.
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(It would take extensive amounts of research and proof to show how the upgraded "tailpipe" caused any failures with the truck.)