Check if the sub-domain directory is completely removed when the domain is deleted. Check /etc/userdomains to see if the deleted domain and/or the sub-domain is still mapped to the main user. If they are remove them, check all the other previously mentioned entries and try again.
Finally, check /var/cpanel/users/[username] to ensure there's no trace of the deleted domain or the sub-domain on any of the lines that start with DNS.
Remember to restart apache or named after you've modifed httpd.conf and remove DNS files or entries.



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