What I did was just punch through the grommit with a philips screwdriver...it makes a very tight hole that you can put a wire through, but is still tight enough to not let water/dust through. This way you can leave the old wiring alone. I wouldn't worry about warranty issues, it's just a poke through rubber. If you're worried about it, you can always slide the wire out and hide it before you take it in ...and if you do it like I did, the hole is not noticeable once the wire's because it's so small.
EDIT: when I say screwdriver, I mean a pretty small one...something small enough to puncture the rubber, and not too big so the hole is tight around the wire.