I got a new certificate, which includes a subdomain, which was on an own certificate before. Now i need to manually remove live/oldsub.domain to symlink it to live/newdomain manually. But when i ran letsencrypt renew --dry-run i got another error, because renew/oldsub.domain.conf still existed.
Maybe there should some option “Remove old certificate for domain X”.
Further i am not sure, what would happen, when you want to maintain two certificates with -d domain1 -d domain2 and -d domain1 -d domain2. At least the paths will cause confusion.