This directory is empty.

You cannot log into cPanel as root. Did you mean you logged in via SSH? What do you see if you log in via SSH as root, cd to the account's public_html directory, and use the ls -alh command?

Also:

I am not exactly sure what you mean that you "ssh'ed" over the files. Did you use SCP? What is the exact method you used, and in what directory did you place the files on the destination server?

If you are the server administrator, you are welcome to submit a ticket and we would be happy to look at this for you.

 

You can be logged in cpanel as root if you go into the cpanel via whm, which I did.

I moved the files from the over server to the new server using ssh and putty and put them all in the same directory as they were on the old server.

 

This is called using the "root override." What I meant in my post was that you cannot log into cPanel directly by entering the "root" username in a cPanel log-in screen. I apologize for the ambiguity.

Again I apologize, but this still does not tell me exactly the method that you used to transfer the files. Did you use the scp command, or the rsync command, or something else? "using ssh and putty" is vague; it would help to know the exact shell commands you used, including all arguments.

Without being able to see the server, what it sounds like is the files ended up in a different path from where you thought they should be, or have permissions or ownerships that do not allow you to view them using the cPanel File Manager. This could happen if the files are owned by root instead of by the cPanel account user, which could happen if permissions and ownerships were not preserved by whatever method you used to copy the files.

I recommend that you submit a ticket so that we may log into the server and investigate this for you. It is very difficult to speculate further about what may have happened without being able to see exactly what you are seeing, and allowing us to log in would be the most efficient way to do that.