Recently I was unable to remove a domain from cpanel after firstly I deleted the dns zone for that domain (using whm)

The error was: “There was a problem removing the Addon Domain” and details of the error explained: “Error from park wrapper: Sorry, you do not control the domain exampledomain.com”

I used the following steps to remove the domain:

1. Remove domain.com from /var/cpanel/users/username
2. Run /scripts/updateuserdomains as root user on the server.
3. Remove /var/named/exampledomain.com.db
4. Remove the virtualhost for domain.com on /usr/local/apache/conf/httpd.conf
5. Remove exampledomain.com from /etc/named.conf

Simple as that!