Do you feel the throbbing and hear the rubbing sound even when not decelerating? Did the throbbing happen when using the brake pedal and/or when slowing with only regen?
I didn't know there was a way to calibrate the regen and I'm wondering how mis-calibrated regen could simulate warped rotors. The Clarity can use its brakes to assist regen--or, when the battery is full, take over completely to simulate regen, but I'd be surprised if your Clarity's regen logic would modulate the brakes with a frequency that simulates warped rotors.
How would regen change with the installation of new brake rotors? It's not as if there are sensors monitoring the state of the brake rotors. Maybe it was new brake pads that confused regen?
If you can, please ask your dealer's service department what they do to calibrate the regen. Looking forward to your report on the results of that re-calibration.