It happens sometimes when you try to create a new addon domain (howto.gr in our example) to receive the error message: 
" Error from domain wrapper: howto.gr is owned from another user "
This can happens due to various reasons and it can be very tricky to resolve. The solution is to completely remove every entry regarding the howto.gr and creating it again. Thus you should edit the following files:

• /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!