GSX doesn't scan the wrong AFCAD.
The AFCAD in use must have been changed and, as explained many times on the forum, in order to speed up the cache regeneration time and the simulator startup time, GSX doesn't check each and every file you have (there might be dozen of thousands), but only the last modification date of the folder the file is located. This means, if the file is renamed, GSX cannot always tell the cache needs to be rebuilt, since the folder last modification date might not change, depending how the scenery has been originally installed. That's why there's a manual cache rebuild option.
The most common cause of a rename of the AFCAD that might not be detected, is if you use 3rd party utilities, even the ones supplied with the airport, depending on what they do) to switch between different AFCAD.
Whenever you see the wrong AFCAD chosen, that's usually solved by selecting "Restart and rebuild the airport cache" option.
And of course, if you have multiple set of AFCADs for each airport, you must have a GSX customization .INI file for each of them.
Depending on the reason *why* there are multiple AFCAD for an airport, it might be required to do the customization or not. If the multiple AFCADs are used only to switch the active runways (for wind reasons), and don't change the parking spots, you can just make a copy of your .INI file with a different name, and edit the name of the AFCAD it should relate to in the [General] section of the .INI file itself.
If, instead, the different AFCAD have different parking spots, for example to use static planes or AI, some work might be required to fix the missing/added parkings.
