I use a reseller account where my accounts get put on one of 4 or 5 servers.
I have one customer who claimed their site files vanished, she reuploaded and a few weeks later they went again!
I moved her to another server and changed her username and password incase someone had gotten hold of the details. Everything has been ok for a couple of weeks but now the files have gone again.
Admittedly they said that it could have been her who deleted some files this time, but its not just files, the complete directory structure has vanished.
No one else has had this problem on any of the servers, she uses frontpages ftp rogram