Let me rephrase to make sure I understood you correctly:
Right now it's Monday game time, for example 9 AM game time. I want to change a flight that departs Monday morning 6 AM and arrives 10 AM, and change it to departing 7 AM and arriving 11 AM, for example. So I go to edit route, and change it. Then I have to apply the route to plane. Fine.
My question is, whether doing this while the "flight is in progress" (it departed 6 am, now is 9 am game time, and flight hasn't arrived yet) will somehow affect the flight for Monday.
Or is it (as I understand it from your reply) that after I schedule the flight for 7 AM, when the game day changes to Tuesday, the system will calculate the Monday flight like it departed 7 am (even if I changed it when game time showed Monday 9 am already)? If that's so, good, because I have spent lots of time waiting for the game time to hit "arrival time" to change something that need reassigning the route to A/C, scared that the flight would get cancelled mid-flight if I did it before the flight arrival time.