When installing an SSL for the subdomain, why does the primary domain lose SSL coverage?

Question

Why does the primary or subdomain lose coverage when I install an SSL for another domain or subdomain in my account? 

Answer

If the subdomain or alias is within the same vhost, you will need to install an SSL that covers all aliases.  

You can look at the SSL host through the WHM to verify if these are individual vhosts or just one. Home » SSL/TLS » Manage SSL Hosts