FWIW and YMMV I've had my F32 flashed both ECU and TCU and have brought it in for standard service many times and my service agent hasn't said a thing.
It kind of depends on your relationship, as my service agent also suggested I tune and mod my car.
I own my car however but for standard service on a lease I would say look into your lease agreement, and if you are tight with your service guy, just ask him.
I hear JB4's and piggybacks can be undetectable but a flash your dealer when running diagnostics will see your flashes.
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