This has happened several times and it's got to stop. Basically, if I'm editing a file, say in the lib folder, then occasionally I go to refresh my site and I get errors and no site. So, when I go back to cPanel to see what's wrong, it says the directory is empty, then when I go back to public_html I realise it isn't empty - it's gone. Thankfully, JustHost has managed to retrieve and restore the folder each time (in this case today it was my core folder).
Any ideas?