Quoted from wayout440:

Your game uses a more advanced electronic "Fliptronics" flipper system, the diagram you posted is an earlier conventional flipper system. The EOS in the older system is actually used to direct which part of a coil system gets current at a given part of the stroke (power or hold). The EOS is not used in this manner for a Fliptronics system. The EOS sensing circuit is used to report information on the status of the switch closure to the MPU.
Examine the connectors to the Fliptronics board. Look for burned or damaged connections and poor solder on the header pins on the board. The power to each flipper is daisy chained. Look for strands of wire broken. The power then comes back into the Fliptronics board at J902, another potential problem.

Quoted from Pin_Guy:

There is one import piece of information missing from this, the last sentence should read...The EOS sensing circuit is used to report information on the status of the switch closure to the MPU, which then provides full power to the coil (via the fliptronics board) to maintain flipper position when the flipper button has not been released.
I think what you are seeing is a gradual weakening of the hold portion of the flipper coil due to a natural heating of the coil when energized, and a failure of EOS switch functionality. A properly aligned EOS switch should open right at the flippers end of stroke; with the flipper in the full upright position, the EOS switch gap should be no wider than a business card.
Since the CPU is in control all of your flippers, both the flipper and EOS switch functionality can be checked in switch edge test to determine if they are being properly read by the CPU.