Does the account have a dedicated IP or it is using the shared IP? If it is a dedicated IP, simply install that new certificate in WHM > SSL/TLS > Install a SSL Certificate and Setup the Domain area.
If you wish to remove the prior certificate, you could remove it in WHM > SSL/TLS > Manage SSL Hosts area. Please ensure to have the CSR, key, crt and cabundle files before removing the existing certificate.
After installation, ensure to copy the /var/cpanel/userdata/username/domain.com_SSL file to /var/cpanel/userdata/username/intranet.domain.com_SSL location and revise as appropriate for the home directory path. After revising, you would then rebuild Apache and restart it:
cp /usr/local/apache/conf/httpd.conf /usr/local/apache/conf/httpd.conf.bak110922