man really wish I knew your car was droped b4 taking it in, otherwise I could have told you to take them off cause the dealer also gave me the same shit with broken axle, then tranny. it's a dealer thing, they will always find away to cancel your warranty. I don't think lowering the car has to do anything with tranny failure. I actually think it's even better since the suspension does not have to travel as much as it would with stock springs. which means the axle won't have to sit as high (stock height) and when you hit a dip or something on the road it won't have to bounce all over the place, it will just bounce one time with after market springs and shocks.
you know what I mean?
Juan, if that's the case, go and get a used tranny for less than $800 and have either the dealer or any other shop to do the job (almost any shop would be fine since replacing the tranny does not involve a lot) ( I did it myself in less than 6 hours )