Hi Rich,
thanks for the report. I assume, this is a FBW limitation. The FBW uses the same flight management platform from the sim and this in-game flight management is very basic and limited.
I have written a short note here, about truncate waypoints from a terminal-procedure. The posting is February, I know but still valid:
I highly recommended to try the same with the WT CJ4 because this mod uses their own flight management and here you have all waypoints in the correct sequence, with exact the same data. Sorry, we can´t do anything for this limitation.
Cheers,
Richard