It's been a few years since I worked in the field so the virtual three-way is a little bit more advanced than I'm used to. But yes I was suggesting a continuity test. One way to do it is that if the boxes are grounded you can test continuity to ground by touching the wire to the box on one side, and then using a meter check to see which wire has continuity to ground on the other side. Power off both circuits before grounding any conductors