There are a lot of causes if the accounts in the server are missing from WHM-->list accounts.
Any of the following will cause the issue.
1) The account is missing from httpd.conf
2) The account has no cpanel user file.
3) The account is not there in the following files.
/etc/localdomains, /etc/userdomains, /etc/trueuserdomains and /etc/trueuserowners
/etc/trueuserowners file specifies the owner of each accounts in the following manner.
4) If the account's DNS conflicts. ie if the domain has 2 DNS entries such as domainname and www.domainname. It may cause the account not listed in WHM-->list accounts.
You can run the following script if the account is missing.
/scripts/updateuserdomains (It won't add the account in httpd.conf, that
you have to add manually)