Cpanel Fix: Error from domain wrapper: .... is owned by another user.

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.

Advanced:

• /var/cpanel/users/username
  Delete any lines containing howto.gr and howto.cphelp.gr (cphelp.gr is the main domain)
  
• /etc/named.conf
  Delete the complete zone definitions (3-4 lines usually)
• /etc/localdomains
  Delete any lines containing howto.gr
• /etc/userdomains
  Delete any lines containing howto.gr
• /usr/local/apache/conf/httpd.conf
  Delete the Virtual Host section and any other entries regarding howto.gr
• /etc/trueuserdomains
  Delete any lines containing howto.gr
• /etc/trueuserowners
  Delete any lines containing howto.gr

Next you should delete the following files and/or directories:

• /var/named/howto.gr.db
• /etc/valiases/howto.gr
• /etc/vdomainaliases/howto.gr
• /etc/vfilters/howto.gr
• /home/username/public_html/howto.gr
• /usr/local/apache/conf/httpd.conf.datastore

Finally login through SSH to the server and execute the command:
/scripts/updateuserdomains

Now when you try to create again the addon domain everything should work flawlessly!