So please, please, keep the communication going. I'll do a better job of scanning all the posts for your comments.
Doubt there will be a build post this weekend - we're heading out of town. In the meanwhile I'll continue to work with Project Magenta support on the disappearing waypoint issue. Here it is again. Flight plan is entered in the CDU and is displayed on the ND:
As you can see above, in plan mode the ND displays all the waypoints entered. The Execute button is lit up, ready for confirmation. When you click it, the waypoints disappear from the ND and are replaced with a straight line flight path from the departure airport to the arrival airport: