Thank you. That bug got me.
I have been experiencing this bug, and thought I might write down some observations I've noticed. If I load a flight plan and click OK, loading it into the sim with only departure/destination showing, the sim will save that state of the now corrupt plan. Then, loading the same plan again does nothing. It pops up a message that the current plan has changed, and would I like to save those changes? I say "NO" and attempt to reload the flight plan again but it does not correct itself. No matter how many times I reload it.
The "trick" with the workaround of loading the fp twice is to load it once,
but don't accept it. Press Load again, and select the same fp again. Then when you come out the waypoints SHOULD re-populate, and you can press "OK" to accept the correctly displaying flightplan.
I've spent quite some time trying to figure this out. That's because if you accept the corrupt fp it is saved to the sim that way. I had to re-install a fresh copy of the flight plans to get the waypoints back. I hope this helps someone else.