I had this issue in the 787, yesterday, as well.
I noted the aircraft will continue to fly to its “missing” waypoint, but the PFD and ND will become “out of sync”.
What I mean by this is the ND will show the missing waypoint as the current destination in the top right of the display. However, the PFD will show the previous waypoint. The magenta line will also cease to update and it will appear as though the aircraft is flying off-course.
On top of all of that, when it’s in this state, if you try to use the “touch” menu on the ND to turn on/off any display features such as waypoints, etc. the menu will not work. You can’t uncheck an option or change anything.
However, the aircraft is actually continuing on its correct flight path. Once it reaches the missing waypoint and switches course to the next waypoint, if there is an actual waypoint shown in the FMC, after a short while the PFD and ND will suddenly refresh. When this happens, the magenta line will be correct, the ND options menu will function again.
I noted, too, that the two FMC displays will not be the same. If I remember correctly, both the left and right displays normally show the exact same thing.
Lastly, as if the above weren’t enough, the autopilot will break when all this happens. I found the auto throttle will no long maintain a speed regardless if you let the FMS control it or you set a specific speed on the display yourself. Nothing I could do would fix that for the remainder of the flight. I also found the AP VNAV wouldn’t hold the altitude and kept climbing past the set altitude. I was able to use altitude hold along with VS to get it to maintain a set altitude.
As a side comment, I used to be a very active member of this forum, but I am exhausted by the absence of 2-way interaction with those in charge. I “want” to write all this up as a bug report, both here and on Zendesk, but at the same time I don’t want to bother. I’m disgusted by how we and our concerns are treated and I swore off this entire forum, but here I am again trying to show my support — not for Microsoft or Asobo, but for all of you users of the sim who are frustrated and struggling.
The lower photo shows the un-synced PFD/ND.
The angle of the aircraft banking is due to this lovely bug STILL being in the sim:
SIGH!