Here is how you remove a cPanel account or remaining parts of cPanel account:
1. Remove the cPanel user account:
#userdel -r CPANEL_USERNAME
#groupdel GROUPNAME
2. Delete the following file:
/var/cpanel/users/CPANEL_USERNAME
3. Remove the site’s VirtualHost entry from /etc/httpd/conf/httpd.conf
#vi /usr/local/apache/conf/httpd.conf
4. Remove the domain from the following files:
/var/named/[domain_name].db (You could remove the zone through WHM)
/var/cpanel/databases/users.db
/etc/userdomains
/etc/trueuserdomains
/etc/trueuserowners
/etc/named.conf
edit /etc/named.conf to remove the domain from BIND
/etc/localdomains