I assume the warranty would not cover the amp if you turn the fan off. But you need to contact Nate to find that out for sure.
It is my understanding that these amps will still work just fine without the fan, but it was put there so the tubes would stay cooler and last longer. I'm sure someone here will correct me if I'm wrong. Having said that, my Renegade 212 barely gets warm (as compared to other amps I've had that get really hot).
Don't do anything until you get an official answer though.