There can be several reasons for why your files seem to have suddenly disappeared.
It is possible someone logged in to File Manager and deleted or moved the files. Check you other folders and check outside of public_html.
FTP access used
If you gave FTP access to someone, they do have the power to delete files. They may have accidentally downloaded the files without leaving a copy, although it is not an easy mistake to make.
Accessing the wrong account
This mistake is much more common than you think. Be sure you are using your cPanel user name, and not "root". This especially applies to those using SSH access.