Having similar issues with flight plans that have points of interest as waypoints. I think of them as invisible. If auto pilot is working properly the aircraft will still follow the flight plan (at least for me it was). This includes flight plans for UK and Japan with POIs as waypoints.
Possible solution: I found that adding an airport as your first waypoint after departure brought back the entire flight plan path even with multiple POIs as waypoints afterward. Tested this a couple of times and it seems to work.