There are a few reasons for this:
Files were manually deleted
Someone could have logged in to File Manager and deleted or moved the files. Check you other folders and check outside of public_html.
Deleted by FTP
If you give FTP access to someone, they do have the power to delete your files even if it's just an accident.
To avoid this, you can create them a FTP account which only has access to a subfolder in public_html. This will allow them the access they need, while stopping them from seeing and changing anything in your public_html folder.
Unfortunately, you cannot give someone access to a directory, but then prevent them from deleting the files there.
What can you do?
If you find yourself in this situation. The best thing to do is to restore from a backup you have made earlier. If the deletion or accident was recent, you can contact Servers Australia support and we can see if we have a backup copy of your site to restore from.