I got this error when I was trying to add subdomains to one of my cPanel accounts. This happens when cPanel doesn’t remove the subdomain correctly and then it thinks it’s still there so when you try to add it back on you get an error. Here’s how to fix it:
1. Remove domain.com from /var/cpanel/users/cpanel-username
3. Run /scripts/updateuserdomains as root user on the server because you changed the above file manually, this will create adjusted cache files
2. Remove /var/named/domain.com.db if the file exists (it doesn’t always)
3. Remove the virtualhost for domain.com on /usr/local/apache/conf/httpd.conf
4. Remove domain.com from /etc/named.conf
Now you can add the domain back on in cPanel with no problems.