I think we're not understanding eachother. I was also referring to day/night cycles and how it is complicated by doing 2 things at the same time. The game must handle both sides being unable to rendez-vous back at the same point at the same time.
I mean, yeah... I just suggested precisely how to solve THIS issue in my previous reply.
You stop the clock for both players/split parties every time one of the two enters in a turn-based mode that could create incongruences. When both players are moving in real time, on the other hand, it simply doesn't matter where they are and what they are doing.