It's a common misconception that tuning boxes will not invalidate the warranty. On more recent vehicles BMW has the car store all sorts of data about the operation of the vehicle, no doubt engine load is in there somewhere. This data is referred to as "FASTA" in the BMW world. This data is automatically passed from the car to the BMW corporate network every time it's plugged in at a dealer.
If you blow your engine using a box or a remap then there's a high probability that a warranty replacement will be refused.
Some units offer functionality to reset engine fault codes to prevent detection, but I believe this does not clear the FASTA data.
I'm not sure how you go about clearing this data. I've played with ISTA quite a bit and not seen any reference to clearing it. Reprogramming the DME may well clear it, which is the process people go through with things like MHD and BBFlash.