We have a domain where the website is hosted with Weebly using their certificate, but I need to protect a couple of subdomains on our own Ubuntu/Apache server. The server hosting the 2 subdomains I want to protect are already set up using an expensive GoDaddy SAN certificate which is expiring soon, and I'd like to use a Let's Encrypt certificate for them instead.
However, reading through all the documentation I can find, the command line for setting this up always includes the canonical name for the domain, then the subdomains. But the actual domain.com/www.domain.com DNS records do not point to the same IP address as the subdomains, and I can't do anything about the Weebly certificate on the main website.
Is this configuration possible?