Understand this topic is old, but if you have not fixed it yet, here we go. The crossconnects will need to be severed, at each car, using an AC relay. Power for the relay will come from the transformer in each car, x1. When the car loses high volt, it will sever the crossconnects, allowing the powered up car to function normally, and vice versa. You can verify this potential fix by pulling the crossconnects (usually two shielded sets) and see how they work.
I am in the process of doing this for a TAC 32, known issue at TKE, they just do not see the scenario as being realistic enough to redo software for it.