I have a site that went down earlier today. All the files disappeared out of the public_html folder. It was empty except for an ftp quota file. Everything was gone, not just the wordpress folders.
At the time, a client was trying to set up an FTP account to do some work on the site. The individual tested the account created on FileZilla, but was not able to connect. She went back to Wordpress to finish up for the day, and when she updated the file to log out, she got a 404 error. Wordpress is not accessible.
She tried to do a manual back up by uploading the wp- folders from her local backup, and then she tried to use the backup buddy backup from the plugin. The browser did not recognize the file importbuddy.php which is supposed to restore the site or import it.
The files in public_html were restored from a backup from Wednesday. We had problems with server permissions getting changed, and worked on troubleshooting that. In that case all the files were intact, but the permissions were incorrect.
The WP database appears to be intact from phpmyAdmin, and I can ftp in from FileZilla.