Separating an established pair can cause stress in itself, as it requires them to make an adjustment to their behaviour and some Corns are less adaptable than others (I've experienced this).
However, I think separating them at a point where they're already undergoing a major move to a new home, is probably the best time to do it. You don't want them to get settled down together, then split them up again in a few months and have the potential trauma all over again. Doing it now, the split is just part of the settling in process. Hopefully you won't see any problems at all.