Hi @Maxim welcome to the community!
The correct answer comes with knowing more about the specifics of your environment.
Would you share some of your configuration information with the community so we can provide you with good info?
If multiple domains are covered by one certificate and for some reason one domain is no longer relevant, that domain can be safely removed from a certificate USING THE PROPER TOOLS AND PROCEDURES.
If a “removal or deletion” is not executed correctly, you WILL hose your system, guaranteed.
That said, you can always use one cert per domain and expand the cert(s) to cover additional domains as you become more familiar with the processes and how they work. OR… just issue a new certificate with the relevant names on it.
Here’s a thread with a similar objective.
food for thought
Rip