The best solution is not always the easiest solution.
I would, as Kaos has recommended, pull the tube off the Electronic Control frame, unhook all of the Thruster wires from the European terminal blocks along with the Lumen Lights PWM connector (your assistant did connect the Lumen Lights power and ground wires to the correct terminal blocks?), the tether wires, and the Pressure Sensor I2C wire. Then pull the rear O ring flange off and pull all of the cable penetrators out of the back plate that are not mounted in the correct position. Using a picture of CW and CCW propellers, put the CC and CCW Thrusters in separate piles then number them 1 though 6 as to whether it is CW or CCW. Reinstall everything according to the instructions. Or
You can change the direction of the Thrusters in the QGC Motor Setup page and I believe that you might be able to change the Pixhawk servo output channels in the Parameters page, however you can change the position of the ESC pwm connectors on the Pixhawk to reflect the actual position of Thrusters 1 through 6.
I would rewire it completely so that it is easily repairable because you never can tell if the individual repairing the ROV knows it is not wired per print.