It will probably affect the fueling and it might require a remap to prevent running over lean. As to the warranty, this what I found in my Owner's Handbook:
The motorcycle’s exhaust silencers are warranted for 12 (twelve) months from the commencement of the general motorcycle warranty. During this 12 (twelve) month warranty period, internal corrosion or deformation of internal baffles are excluded from the warranty. After this 12 (twelve) month period, the motorcycle silencers are excluded from the terms of this warranty.
I take that to mean that the silencers can be replaced without affecting the warranty on the rest of the bike.