Quoted from Schwaggs:
Confirm the magna slings still work when the flippers die. This will prove the node board where the flippers are connected, still has power and is being controlled by the CPU node.
The flipper switches are connected to the cabinet node board. Maybe the cabinet node board is losing connection with the CPU Node?? Try reseating the RJ-45 connector on the cabinet node board and the one at CN3 on the CPU node board in the backbox.
On my game, the flipper buttons are wired to a node board on the playfield. I realized this when I hade the cabinet node board removed, and noticed the flippers still worked.