Correct me if I'm wrong but, my understanding is by unplugging CN2 you are disconnecting the wiring to the flipper coils. Plus, 50V from the PPB board and 8VAC for your hold up flipper voltage. So I'm not sure if that's going to tell you anything because, everything is disable.
CN2 pin 1 - Left flipper coil
CN2 pin 2 - Left flipper coil
CN2 pin 3 - Nothing it's, keyed
CN2 pin 4 - Right flipper coil
CN2 pin 5 - Right flipper coil
CN2 pin 6 - 8-9VAC for flipper up
CN2 pin 7 - 8-9VAC for flipper up
PPB board J7-1 feeds 50V to----> CN2 pin 8 - 50VDC flipper power
PPB board J7-5 feeds 50V to----> CN2 pin 9 - 50VDC flipper power
Check J7 pins 1 and 5 for shorts, Check CN2 pin 8-9 for shorts.
Flipper coils measured right? So that's good.
Flipper diodes are installed right but did you measure them? Did you use new ones? With the game off. DMM on diode reading, cut a lead and you should get .4 to .6 in one direction and open when you reverse the leads. Easiest to just install new ones. Should be a 1N4004. Right over the lug is fine. Power to the banded side, middle lug.
Robocop's flipper coils didn't use an eos switch, but what about the flipper cab switches? Should be normally open. The .1 cap is for spark reduction by the way. It should have a lane change/high score switches attached. Look for shorts. Doubt it's an issue, but I would elimate everthing at this point.
Follow the flipper coil wires all the way up to the backbox. Check the wire harness. I know data east put a 2 pin connector that disconnects 8v flipper up power before it goes to the backbox. What about the flipper coil wires? Did someone cut them at one point and added a connector from the backbox? Is it shorted?
The RY1 flipper replay could be suspect on the cpu board. It turns ground on to the flippers. If it fails, the flippers won't work. It works with Q80. You should hear it click when the game starts.
At this point, I'm leaning towards bad driver transistors on the flipper board. Since the diodes were reversed and power was applied, it shorted out the the driver transistors associated with both flippers. When this happens, the fuse(s) will blow immediately.