But the point of the "Restart Couatl and Rebuild Airport Cache" is to fix the AFCAD which it isn't doing at all.
That's not what that function does. The "Restart Couatl and Rebuild Airport Cache" cannot magically "fix" GSX to let it use the right AFCAD.
The one and only reason for that option to exists, is to let GSX detect a change in the file used when you *remove* a .BGL after the last time the cache was created, because removing a file doesn't change the folder last modification date, which GSX use to know if something has changed in the Scenery Library, because it's obviously much faster checking this way, rather than going through each file (could be thousands of them) at *each* start. That's the ONLY thing that option does: helping GSX changes due to manually removed files, which cannot be otherwise automatically detected.
To have GSX pick up the "right" AFCAD, instead, you must be sure the priority rules are respected, which means the scenery you want to use must be on an higher layer in the Scenery Library.
In addition to that, if a scenery developer use fictional ICAO codes for auxiliary airports like military bases or seaplane/helicopter bases inside or very close to the main one, you must exclude them using the "airport_visibility_xxxxx" command, as explained in the GSX manual.