If you change the AFCAD file name, you'll lose GSX customization.
If you overwrite the one that comes with the scenery with a file with the same name, reinstalling the scenery, GSX or the Addon Manager or installing a GSX Major update, will restore the FSDT AFCAD AND WILL BACKUP your modified file.
This means, the correct procedure to edit our AFCADs is:
1) Base your modifications on the most current version of the AFACD that comes with the scenery. Reinstalling the scenery or GSX or the Stand-Alone Addon Manager will get you the most current AFCAD for all your installed sceneries. Once you are sure you have the most current version of the AFCAD, you can start modifying it.
2) Save the file with ADE using the same name as supplied from FSDT installer.
3) After you reinstall the scenery, GSX or the Addon Manager or install a GSX Major update, look for the backup of your file that was made by our installer (there will be a current date/time appended and a .BAK extension), remove the FSDT AFCAD and manually rename your backup to the normal AFCAD name. This will restore your changes.