Cortex has two internal PTCs that protect from motors drawing too much current.
One protects ports 1-5 and another protects ports 6-10.
If something like a shorted motor wire keeps tripping one of the PTCs, then it could explain entire side of the robot not having the power at the same time.
Check your motor and controller wires for any damage, try to replace or connect one motor at a time to eliminate if any of them is damaged.
In the worst case one side of the Cortex could have a blown PTC. You may need to move all motors to the other side, but don’t do it until you are sure the motor has no problem, or the other side could get damaged too.