Thanks for the replies guys. Right now it seems that you guys are fine because nothing has happened. But, what if your motor blows and you have a tune and drop in filter? I'm sure BMW will put the blame on the motor failing on the filter (isn't filtering enough) and/or the tune (making the engine run out of spec).
I still want the safety that the CPO warranty offers. I guess I'm going to have to call my dealership
2012 328i Sport Line: H/K + SA