Hi Rick,
It all depends on how your power stage is designed. Typically, there are 2 major use-cases:
- Regenerative Breaking (e.g.: EV, Trains, Trams, etc) where it is actually recommended to push back into the battery or network/grid the recovered brake energy. A typical schematic is shown below (source here). In this case the energy is pushed back into the grid via the T1/T2 transistors controlled based on the polarity of the network.Using the PWM technique you can modulate the UT that is pushed back into the network to about over-voltages.

- Resistive Breaking (i guess the case that's interesting you) where you are not allowed to push back the energy into the network but rather dissipate it as heat on a local resistor network. This case is similar with the MotorGD DevKit schematic.

In this case, you typically have a diode protection circuit that ensure you can't push back the voltage/energy into the battery/grid, hence you do not have to take any additional precautions to protect the power source. Nonetheless, you need to dissipate somehow the energy, hence you have a break transistor to modulate the rate of discharge.
Typically, you need to implement a simple PI controller that computes the difference/error between the reference DC Voltage Link allowed from the power source the actual DC Voltage recovered from the motor. Then based on the error value you open the braking transistor more or less.
In conclusion: if you do not have the diode protection for the power supply, and you need to use the resistive breaking, then you need a method to disconnect the power supply - perhaps using a simple IO relay switch.
Hope this helps!
Daniel