A system and method for configuring and controlling towed vehicle brakes via a secondary brake control system controlled by a towing vehicle primary brake controller by responding to events or errors through adoption of different structural configurations and modes of operation so that it may adapt to use different blends of input from the primary brake controller and/or a secondary brake controller of the secondary braking control system, while preventing the use of the secondary braking controller from causing errors or failsafe mode activation of the primary brake controller. Signals from the primary brake controller may be modified before they reach braking actuators of the towed vehicle, and/or the primary braking controller may be completely disconnected from the braking actuators while a dummy load simulate feedback that the primary controller needs to receive from the brake actuators.