If you are in the midst of building and/or modifying one of your missions, be wary of editing the Waypoints of your flights.
If you have a -waypoint option- tab set for 'Patrol' and you change the -waypoint- tab from 'Normfly' to 'GAttack' without changing the -waypoint option- tab back to 'Normal', you will get a small "Standby Mission Loading" notice on top of your map with only waypoint markers and no objects as well as corrupt the mission file.
just found that out. Luckily, I back up my mission files.
happens in stock/4.11.1m and HSFX.