Ghost domains

Hello, I have a problem that I have not encountered before. One account that has domain.com assigned to it, there should be more domains under that account in "Domains" or "Addon Domans" but it is empty. Under "Redirects" I can see those extra domains and also in "Emails". The /var/cpanel/users/domaincom file has those domains listed and they are also listed in httpd.conf. The reason why I noticed this is that I was going to remove all those extra domains and just use the main domain for that account and move the other domains under their own accounts. How can I fix this without having to delete everything manually? I'm running CloudLinux 7.8 and the latest version of cPanel, everything is up2date. Thank you.