Issue :
Several add-on,parked,sub-domains under a domain exist on the server but they are not listed in cPanel. Changing themes did not resolve the issue either.
Fix :
This can be fixed by deleting the .cpanel directory for the user. Once that is done, re-login to cPanel and you should be able to view everything.
If this does not resolve the issue then force update cPanel by running the following :
/scripts/upcp –force
Note: You need ‘root’ access to the server to run the above script.