Thanks for all the help from everyone more electrically competent than me!
This weekend (yesterday evening) I confirmed that this works. There are 8 flashers in the BK2K backbox (as well as playfield flashers but the backbox ones were good to see the results) that flash with flipper power strokes. 4 sets of 2 flashers for 3C, 4C, 6C and 7C. This modification fixed all the flashing with flipper power strokes. Here is what I did:
1) Cut one (the non-banded) side of diodes D3, D4, D6 and D7 and lifted the cut side off the board to prevent accidental contact. Ideally I guess the entire diode should be removed or the cut leg insulated.
2) Built two custom connectors (seen in the photograph below). Both of these are pass-through connectors for the actual wires with the ability to "tap into" that portion of the circuit. It is also possible to do this with IDC "Z" connectors but I don't have any of those as I prefer to use the trifurcon crimp connectors. These are used on 5J4 and 5J12 but 5J12 is strictly not required (see below).
3) Connected an additional wire to 5J12-12. It's +50V and continuous with 5J12-11. This is an unused wire in the IDC so you could just put the wire into the IDC. I don't have IDC tools. Connected this wire (yellow for YEL-VIO) to the banded side of 4x 1N4004 diodes. Connected the non-banded side of each of the 1N4004 diodes to the appopriate VIO-*** wire that is the drive wire for the 3A, 4A, 6A and 7A that was "tapped into" the 5J4 connector.
Fired up the game and the flipper power stroke flashing was gone. On BK2K it was particularly annoying as the return lane has flashers that were problematic.
Hope this helps. I attached a photograph of the "hack". I have my flame retarding jacket on. For those that wish to flame ... FLAME ON! The only invasive part is the cutting of the diodes D3, D4, D6 and D7 on the auxiliary power driver board. That's why I was asking if it's required. Unfortunately it is required. Otherwise there's no other board wires connected. Only the 1x wire from 5J12-12 split to 4x diodes to 4x wires on 5J4.
Guess I'll be building these for my Whirlwind and Rollergames as well.
Again ... thanks to everyone for the help. I'd noticed this a few years ago when I put LED flashers in my Whirlwind but never understood why. At that time I just put incandescent flashers back in and it has remained that way since then. Not any more!!!