Flying multi battery

If you manually take over the aircraft to land the waypoints will get out of sync. In this case you would need to review the blue verification line at the time of mission upload to make sure it is accurate. If it is not what you expect, you should use the Manual Restarting Point feature:

https://support.dronesmadeeasy.com/hc/en-us/articles/115005940746-Manual-Restarting-Point

This will allow you to select any corner to restart you mission.