Best analysis so far.....and very scary.
If this turns out to be the basic scenario then it is heartbreaking.
Part of my routine coming on-shift at an EMS base in Texas was to take the Waypoint List out to the aircraft and manually check each Waypoint that was entered into the memory....to ensure each matched the Base Record.
When I encountered one that was not on the list I deleted it.
A Paramedic saw me doing that and raised hell when I deleted a former Paramedic's house Waypoint from the memory. He refused to consider my advice to him.....that he get it blessed by the GPS Waypoint God and have it added to the approved list and I would be glad to re-enter it.
We had a process we used to confirm the accuracy of each Waypoint entered and maintained a record for each one that had not just the Identifier and Coordinates but other information as well to include the Elevation of the Waypoint, location description in general wording, and also references to other Navaids such as VOR's, DME's, and NDB's. That way there was no confusion and at any time the information entered could be confirmed as accurate.