Nice software, but we MUST have an NOT to update ADE files, since most users have them customized.
Check better, the Live Update obviously knows the name of the AFCAD for each scenery is updating so, when it finds the AFCAD on your disk is not the same as the one on the server
it makes a backup, in a "backup" folder under the scenery folder.
So, as long as you keep the AFCAD name the same as the original from FSDT, you can be sure your changes will be backup. Using different names for the AFCAD, it's really a bad idea for our sceneries, because the name of the AFCAD is what triggers the GSX airport customization, which will disappear if the name is different.