If accounts are not displaying in whm make sure the entry for the domain is there in following files --

/etc/userdomains
/etc/trueuserdomains
/etc/httpd/conf/httpd.conf
/var/cpanel/users/$user -- DNS=<domain> should be there
/etc/named.conf

In addition to that, the username must exist at

/etc/trueuserowners
/etc/passwd
/etc/shadow
/etc/group