If you are getting the above error then just remove the domain.com entries from the below files :

========================

/var/cpanel/users/username

/scripts/updateuserdomains

/var/named/domain.db

/etc/named.conf

/usr/local/apache/conf/httpd.conf

/etc/localdomains

/etc/userdomains

/etc/trueuserdomains

/etc/trueuserowners

/etc/valiases/domain.com

/etc/vdomainaliases/domain.com

/etc/vfilters/domain.com
========================

And if still does’nt help then try enabling this option from WHM

Main >> Server Configuration >> Tweak Settings

Allow Creation of Parked/Addon Domains that are not registered

and then edit  the cpanel.config file
===========================
root@server[#] vi /var/cpanel/cpanel.config
autocreateaentries=0
:wq!
===========================

That’s all this will do it.