This is a random occurrence (bug??). At times, I will load up a plan I made either from Flight Planner, or one that I have saved local. It will show ALL of my waypoints, which can be a lot, lol, however, more then once, it will revert to the departure and destination airport and the rest of the waypoints will be gone.
As mentioned before, cannot reproduce it, it occurs randomly.
I have reloaded the flight plan, and it shows all my waypoints still there and may nor may not follow it.