The short answer is yes your warranty will be affected. However many dealerships are aware of remaps and are not scared of them, some even offer them! It is important to note that a manufacturer cannot refuse a warranty claim on your car because it is remapped, they would have to prove that any failure was directly caused or affected by the remap. This is always a grey area and some people prefer the "head in the sand" approach where other people are more up front with their dealers. Remember that a dealer wants your business so they may turn a blind eye.
There are alot on here who have mapped new cars. My S3 is a 12 plate but everytime it needs to go into the garage I upload the original map just to be on the safe side in case they turn round and void the warranty. If your friendly with your tuner ask him if he can upload the original map when needed. This is what I do for afew of my customers when their cars go into the dealers.