If you're worried about warranty claims, just get a second Trionic box from the wreckers, er, dismantlers, and send that one out to the tuning company. That way, you ca always change the ECU for the original, untampered one before you have your car serviced.
[note: This could also be a wise thing to do for track day regulars worrying about voiding the manufacturers' warranty. As according to camanufacturers, the ECU records just about anything: how often the rev limiter has been triggered, in the case of advanced vehicle stability programs acceleration rates, 'excessive' vehicle speeds, how often you've been to the red light district, er...]