If your cPanel accounts missing on List Accounts WHM > List Accounts but It was created already. It may be corrupt the following file. Anyway, verify the following files entries.
Check /etc/userdomains – this file should contain the the domain and username that’s missing.
/etc/userdomains This file contains all subdomains as well but those aren’t relevant, it must contain the main
domain and username.
/etc/trueuserdomains this file should also contain the domain and user in the same format as above. This file only contains the main domain or the domain under which the cPanel account was created. Some clients create cPanel accounts for subdomain.domain.com (which is fine) for a variety of different reasons. If subdomain.domain.com is missing from your list of accounts it should be listed in this file.
Check /var/cpanel/users/USERNAME. The USERNAME should be replaced with the cPanel account’s username. The file should contain a lot of info, but has to have the following lines:
OWNER=root (This will be set to ‘root’ unless the account was created under a reseller).
Check the Apache configuration file /etc/httpd/conf/httpd.conf and make sure that a virtual host exists for your domain. Try to rebuild apache /scripts/rebuildhttpdconf
Finally run the following script to update user domains.
If your account still not available in your WHM then it may be account deleted or termiated. Try to recreate account force.
Userdata folder missed user entries ?
Is your /var/cpanel/userdata directory missed all the user details? Please use the following script to rebuild missed user entries.