Check diodes on the flippper coil, one of them could have broke loose or burned open.

There is no tie between the GI and the flashers. So one won't effect the other. As far as the fix for the flashers goes you can, add a incandescent bulb to one the circuits if there are more than one bulb in the circuit. So if there were 2 bulbs on the play field and one in the back box on a circuit just leave the bulb in the back box incandescent and the 2 LEDs on the play field will work correctly now. Or you can remove the diodes on the aux power supply and add new diodes too the coils of the same circuit. This allows you to have all the bulbs on the circuit be LEDs. As for removing the diodes I would just cut them off of the board so you don't have to remove the aux power supply from the game. If you need help with part identification and location just let me know.