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= should be there
/etc/named.conf
In addition to that, the username must exist at
/etc/trueuserowners
/etc/passwd
/etc/shadow
/etc/group
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