BMW does has the ability to see when codes were cleared and if it was a BMW ISID, GT1 or non recognized tool(i.e. aftermarket scanners).

One of my techs was shunned(and charged back) by BMW for clearing out a code with a Matco scanner then re reading the car with the ISID and claiming a repair.

I doubt they well mess with you over clearing tuner codes, they've come to terms thier product isn't perfect.