This article discusses how to resolve issues where the WHM reseller list has disappeared however they still exist in Apache’s configuration and the users’ directories still exist in /homeSymptom
Resolutions
1)/var/cpanel/users/ -

/var/cpanel/users/username should have the following syntax per line "DNS=domain.com" line. If not, edit this file and change the line to DNS=domain.com
Secondly, be sure to check that the DNS zone above exists in "Edit DNS Zone" in WHM. If not, add it via "Add DNS Zone" in WHM.
2)/etc/httpd/conf/httpd.conf
Double check that there is a VirtualHost container per domain in /var/named/
3)/etc/userdomains –

/etc/userdomains should have the following syntax per line “domain.com: user” where user is the reseller. If not, edit this file and change the file to match.
4)/etc/trueuserdomains –
/etc/trueuserdomains should also have the following syntax per line “domain.com:user”where user is the domain owner user. If not:
mv /etc/trueuserowners /etc/trueuserowners1
/scripts/updateuserdomains
/scripts/updateuserdomains
Reference Links:
http://forums.cpanel.net/showthread.php?t=48765
http://forums.cpanel.net/showthread.php?t=48943
http://forums.cpanel.net/showthread.php?t=47888