Multiple battery mission fail

Just flew a mission requiring 3 batteries, first thing I noticed was the app saying Flight 1 ended, battery changed? Start flight 2. So I launched the mission alltough I got these confusing prompts. Everything went of with out a hitch until the battery switch. Swapped batteries as usual, but this time it prompted to start flight no 3, I went ahead and launched and the drone just goes back to start from the beginning, not recognizing the blue abondomnet point where it should pick up. Cancelled and tried again and the drone refuses to pick up where it left of, it will only go back to start of project and not the abandonment point. I did hit the pause button and return to home on the first flight as battery was getting low, other than that I did everything the way I usually do. What might have gone wrong here?