All pdf files links lost after cleaning \AppData\Local folder

I am using Mendeley Desktop on Win 7. It is a good citation management software. And by using the File Organizer function, I put all the downloaded journal articles into a local folder and have them sorted. But after I cleaned the \Users\AppData\Local folder, it seems Mendenley has lost all the pdf connections. There is probably little hope to restore it automatically. So I suggest Mendeley perhaps could back up this pdf association automatically, or may be consider move it to another 'permanent' folder, or requires Administration Level Access to modify these important files. Thanks,