The CB should be sized to protect the motor and the wiring. The wiring should be sized for voltage drop at the nominal (non charging) output voltage at the max flap lowering airspeed (motor load) current draw. Typical wiring size would be 20 AWG for a typical run length, and CB sizing of 5-7amps. If you have too large a voltage drop under load the motor will stall, draw higher current and pop the breaker. Could possibly get away with a 2A CB but increases the risk of CB pop on approach to land with initial flap deployment.
KT