There was a TSB issued by BMW to fix this problem. On an automatic they reprogramed the transmission. While more rare on the manuals it is usually a mechanical fault and not covered by the TSB. While there is a chance that you could corupt the ECU it is a rare occurance. I have heard of 1 instance where a Shark Injector caused the ECU to corupt and the owner was then liable for the replacement of the component. If a part is damaged in the course of the repair then I would think that the stealer would need to repair the vehicle to it state prior to the work being preformed. This is just my opinion please check with you dealer.
"It's not because I'm an aggressive driver, it's because I'm an idiot" actual quote from my wife.