[Al Skierkiewicz]

fox,
There is no protection. What you have observed (and what takes place during brake mode) is that the diodes that are a result of manufacturing in MOSFETs will conduct energy from the motors to the power supply or to a short with multiple FETs turned on. When power is supplied to the controller output, reverse currents may flow in the interface electronics and the microproc on board the controller. Many teams have reported controller failures as a result of this very same mistake just this year.