More info needed. Are you running conventional or TMCC/DCS?
Assuming that the center rail is insulated from that of each loop at some point within the crossover:
If you run purely DCS/TMCC, the voltages from both Z-4000 outputs are likely to be set the same and the short connection between them via the locomotive or passenger car pickup rollers won't matter.
If you are running conventional, then you need to take care to have the voltages of both loops set the same when the train is crossing over. And you wouldn't want a step-change in speed then, either.
Because the source for both tracks is the same Z-4000, no phasing issue exists.
