The dealership can easily charge a customer 1 hour of labor to overwrite the OTT tune with a factory Toyota tune, to do appropriate diagnostics.So much of warranty issues being processed or denied are based on ones personal relationship with a dealer. The cool thing is with my research I have never heard of a single person being denied a warranty claim with an OTT tune.
If you tell them don't reflash the ECU, it's going to draw suspicion.