I was wondering if just replacing the Factory muffler with a flowmaster voids the factory warranty for my truck? I have an '03 with 6k miles on it so i don't really want to void the warranty.

not unless they can prove it caused the problem, which is very hard to prove, i have had my truck in after intake and exhaust with no problems, but i have heard of people having problems with a chip....

As long as you don't mess with the O2's and the cats there shoul;dnt be a problem unless a pipe rubs up against something or you bring it in with the tach stuck up in the red line

the only time i have seen a custom exhaust trip an engine light was from running straight pipe. i have a gibson and light has never turned on because of exhaust. the only thing is if it isnt supported right and it twist and cause an exhaust leak or even possably crack the exhaust manifold.

if the chip is a warranty problem couldn't you just remove it prior to taking it in to the dealer?

Yep,,,,98