I am trying to set up certs for a host that has about 220 hostnames (with an without www, some subdomains, some stating subdomains etc) so that I have to split the list into 3 certs and use SNI. When putting the priority domains at the top of the list they end up in the first cert and the cert dir in /etc/letsencrypt is the name of the first domain in the list.
However for the other certificates, the name of the dir is determined by the position of the 101st domain in the list, which means that this will change if the list is modified, for example if there is a new subdomain inserted (this could be fixed add domains only at the end) or if a domain is deleted from the list (and everything after that goes up 1 line and the cert dir names change).
The best workaround for this would be if it were possible to set the dir name of the created cert to a fixed name (e.g. cert1, cert2, cert3), but I think that is not supported by the certbot options.