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Are you trying to create an addon domain or Parked domain? Or are you trying to create an account in WHM but getting error that says:

The domain already exists in the Userdata

or

Domain already exists error in Apache Configuration

If you are a Reseller, this usually means that a different user still has that domain on his/her cpanel account. So you should contact your Host for assistance in verifying the actual status of the domain on the server.

However, if you are root, that means that the domain was not properly terminated from the server.

You should look into these places to remove all traces of the domain from the server to create room for it to be created afresh:

/var/cpanel/users/$user
/var/cpanel/userdata/$user
/var/cpanel/databases/$user.json
/var/named/$userdomain.db
/etc/userdomains
/etc/trueuserdomains
/etc/userdatadomains
/etc/localdomains

Once those Traces have been removed, run the following commands:

/scripts/updateuserdomains
/scripts/updateuserdatacache
mv /etc/apache2/conf/httpd.conf /etc/apache2/conf/httpd.conf.bk
/scripts/rebuildhttpd.conf
/scripts/restartsrv_httpd