Check user cPanel config
# cd /var/cpanel/users
Make sure the primary domain exist inside DNS
# nano -w username
DNS=domain.com
Or backup old user cPanel user
# cp /var/cpanel/users/username /var/cpanel/users/username.backup
# nano -w username
DNS=domain.com
Domain name should appear inside List of Accounts now.
If user already exist and all settings are correct, run:
# /scripts/updateuserdomains
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