I would be quite surprised if you had to do anything. Personally, to be sure, I would switch back into P mode (Phantom 3 x) after the first mission completed. COMPLETED. Then switch back to FPV mode, back to Waypoint, switch back to F mode, load 2nd mission, run, and as long as you are aware of the waypoint 1's starting position in relation to you, I think you're good to go. Make doubly sure that Mission one waypoints have been unloaded. (The "X" will erase all waypoints too, but that is an edit function usually).
I have thought of trying this, but after my first mission completes, I'm usally looking at less than 60% battery and I simply will not fly another consecutive mission usually with that being the case.