Introduction
There are various reasons that you may want to delete an SSL certificate. It is possible to do so via the WHM interface.
Procedure
1) Log into WHM and navigate to (WHM >> SSL/TLS >> Manage SSL Hosts)
2) Scroll down and find the SSL certificate in question. Select "Delete" from the far right to remove it.
For more information, please see the following documentation.
https://docs.cpanel.net/whm/ssl-tls/manage-ssl-hosts/