You have a certificate with a couple of alternative domain names added to it, but want to get rid of some of them while keeping others? The parameter --renew-with-new-domains is what you want. This is how you use it:

certbot certonly --cert-name "maindomain.com" --renew-with-new-domains -d "maindomain.com,alternative1.com,alternative2.com"

This will renew the certificate maindomain.com with the domains maindomain.com, alternative1.com and alternative2.com. Any other domains that had been included in the certificate before will not be included in the new certificate. If you execute it like this, it will ask you for the verification method and parameters interactively. Alternatively, you can also configure this with parameters like -a webroot --webroot-path "/var/www/” .