I remember this scenario (fpl deleted) is most common when one is not flying a "conventional" procedure. This is usually setting up a visual traffic pattern (or visual approach, whatever it might be), which has no missed approach procedure, hence no more waypoints after dest. To prevent fpl deletion we manually insert a waypoint after dest that is coherent with the intended flight path in case we go around. You will have a fpl so long as you don't sequence all waypoints in it