The problems arise under one of two conditions:
If teh controller's LVC is higher than the battery's voltage at that point, the controller will shutdown. If the controller's LVC is lower than the battery's voltage will ever be, there's no problem there.
If the battery's BMS HVC is lower than the battery's voltage at that point regen current is flowing into it, it will shutdown the output, disconnecting the controller from the battery. Probably it will reenable the output shortly after this, once the voltage drops below HVC. If the regen voltage is never higher than the battery's HVC voltage, it's not a problem.
These things aren't normally an issue with a controller and battery that are rated to work with each other. Like a 36v battery on 36v controller, or 48v b/c, etc.