Of course, I'm not going to name them exactly the same as the FSDT one.
That's precisely the issue, if you use a different name for your own custom AFCAD, the update will consider it as an "redundant" file, since it's on your system, but not on our server, so it will just remove it.
The issue is, sometimes as part of an update, we must remove files too so, it will be very complex trying to sort out which files were ours to remove, and which files were added by the user (in order to backup them), because we would have to keep an history of all files we ever distributed, even when there are not needed anymore.
If, instead, you use the same name of the FSDT one, it will be backed up. And, using the same filename, will not lose you the full GSX customization.
Thankfully I also know that I can edit the GSX customization file to work better with my own setup.
The issue is, the GSX customization you can do from the GSX user interface is not as complete as what we can do with our code so, you want to start with our baseline and improve on that, but in order to do that, the AFCAD filename must match.
As per the "DONTUPDATE" that isn't located anywhere in the GSX manual, it's not that I don't want my airport scenery updated, it's more that I don't want my custom airport file messed with.
It's not officially documented, because I still believe you want to have the AFCAD updated and yours backup so, you can decide if you want to retrofit your changes to our new file or not, depending on what you did.
In any case, we updated the Updater today, so you'll see an alert if the AFCAD is going to be overwritten, offering you a choice. If you choose to update, it will be backed up, otherwise it won't do anything, but it will still update the rest of the files in the scenery folder if needed (unless you made a DONTUPDATE file). But you must use the FSDT name for your AFCAD, otherwise your additional file will be removed.