Already discussed here:
http://www.fsdreamteam.com/forum/index.php/topic,6753.0.htmlAs the other thread clarified, nothing you made is ever lost, and a backup is always made.
If are used to add your own approaches, the better option would be making a separate AFCAD containing just the approaches, and put it on an higher layer in the Scenery Library, it's best if you just make one folder with all your modified AFCADs there, so you need only one area in the Scenery Library.
You can also use the same method for the whole AFCAD, so you can simply stop worrying what happens in our scenery folder, because your own AFCAD will take the precedence and won't be overwritten. However, you must be sure your AFCAD is still named as the original one from FSDT, otherwise you will lose any GSX customization we made for that airport, and you might miss eventual updates we made for it.