OK, so I had time and tested it yesterday. Here are my findings, pretty simple to be honest:
-
If you let the autopilot be then it does indeed navigate through the “missing” waypoints. Even though they are not in the FMC and don’t appear in the flight path, these waypoints still appear in the upper right corner of the ND and the autopilot knows where to go. Just do not interfere in any way, however confusing the display may become.
-
While the autopilot flies towards such an “invisible” waypoint, part of the ND freezes. Namely, the flight path. Thankfully, the other displays remain working, so you can keep track of which waypoint you’re flying towards and what the distance is.
-
The ND unfreezes after the plane passes two “legit” waypoints again (so waypoints that appear in the FMC).
So in short, it’s actually possible to complete these journeys. Last night I had a flight that had 3 missing waypoints in the FMC, and there were no problems, apart from the flight path always freezing. Since the approach phase usually contains many legit waypoints, the ND unfreezes towards the end so it’s not hard to navigate and land properly.
I think that in the end this is the very same problem that causes the G1000 screens to freeze. I guess the Garmin systems have the same issue, they simply don’t recognize waypoints and freeze, but recover then the plane passes a “proper” one. G1000 Screens Freeze - Bug Reports / Aircraft & Systems - Microsoft Flight Simulator Forums
I guess this is an AIRAC implementation issue. Hopefully it will be fixed sooner rather than later and we won’t have to wait until SU10. 