When running /usr/local/cpanel/bin/checkallsslcerts the following error is received:
Error 400: Bad Request
No cPanel user controls a local domain called “domain.com”.
The issue is noted when attempting to obtain an SSL certificate for the server's hostname. The request is unable to property route the HTTP DCV which prevents the certificate from being issued.
Rebuilding and restarting Apache should allow for the certificate to be issued.