I think since SU8 adding or removing waypoints to your flightplan often dont work. Waypoints you have activated through the world map filter.
I am having the opposite results. For several months before SU8 I was forced to enter waypoints in the Garmin 1000 NXI. Starting a few weeks ago with SU8 I am now adding most waypoints using the World Map again after showing waypoints using the filter dialog.
I get a similar issue, also.
Submit a flight plan using the world map, then once in the air can not modify it. Clearing, or adding waypoints.
This is not 100% every time, but it does happen.