This sounds like a huge mission. It would help if you had some screenshots or something. The DJI SDK says that you can't have points that are further from each other than 2000 meters. In the case where this happens in a Map Pilot layout we usually break the long leg up into 1999 meter segments.
We haven't heard of this happening for a pretty long time since our workaround seems to work well. It is POSSIBLE that your were right at the edge of a 2000 meter segment and the GPS inaccuracy of the homepoint put it over the 2000 meter limit at the time of the layout. The fix here would be to move the aircraft towards the point where the flight path is being resumed.