One option which might not be the safest is the Certbot
--allow-subset-of-names option (which treats the renewal as successful even when not all names can be renewed).
A more correct option is to specify the particular names that you want to be included in the cert, as well as the cert name. If the cert name from
certbot certificates is
www.transsee.ca then on that server you could run
certbot certonly --force-renew --cert-name www.transsee.ca -d www.transsee.ca -d transsee.ca
And on the other server you could run
certbot certonly --force-renew --cert-name www.transsee.ca -d doconnor.transsee.ca
The one thing that might be confusing as a result on the second server is that the cert name would be unchanged, so the cert on the second server would be named after a hostname that wasn’t actually covered by the cert.