The short answer is yes, they will void your warranty if they find out you tuned it.
However, the stock engine configuration is saved on the Cobb, so if you ever have to take it into the dealer you can revert it to stock and they will not know you tuned it.
Just be smart about how far you push the tune!
(SOLD)2010 Alpine White 335i
- Sports Package, Premium Package, Navigation, Comfort Access
2016 Infiniti 3.0t Q50S