I am not aware of any software settings for disabling the beeper on the VEC controllers, therefore I don't think there will be a simple way of stopping the beeping during regen.
Dismantling the controller and physically disconnecting the beeper unit may be the only way to stop it completely, but it may be possible to block its sound outlet hole to greatly reduce the sound level. However, dismantling the controller might invalidate any remaining warranty.
It would not be an issue if the controller had been programmed to only emit the 15 beep brake warning code when the throttle
and the brakes were both activated simultaneously, then it would only beep if you still had the throttle applied during regen
or if you inadvertently tried to power the motor without realising that regen was still engaged.
Alan