Quoted from wayout440:

Check the flipper sensor board. The purpose of the sensor board is to determine when a flipper coil was enabled via the flipper cabinet switch, convert the 48v signal to a manageable voltage for the switch matrix via an MCT6 optocoupler, and then send the signal back the return line of the switch matrix.
Since neither flipper works, you've probably lost either ground or power to this board, or it may have simply became unplugged.