If you paid for 100k of warranty, I don't see how they could refuse to repair a defective part if the vehicle still has under 100k miles on it. They could replace the transmission with a 4L80E and then your worries will go away. If it's the GM warranty, I don't think they'll refuse to repair anything unless they can prove you intentionally damaged the transmission. It's not like your running a stall convertor or something. If you modify the transmission then they might refuse to repair it.