Having Trouble Selecting What Waypoint to Start a Mission @Dave_Wynne Check out this link to a similar thread with @TriBar having the best answer the the mission battery change question.
Another flyer suggested breaking down the single mission into multiple smaller missions with the battery change happening between them. Otherwise if you randomly decide to come back for a new battery, you will have to write down which was the last waypoint and then resume the mission at the next one after the change.