I first set up different certs for each of my domains, then realised I could do one cert for all. But when I did that and selected to replace & renew a current domain I couldn't find where the new multi-domain cert was (all those in /etc/letsencrypt/live were symlinks to archive).
Then to make matters worse, when I tried to run again with --cert-path to try and put the new multi-domain cert somewhere else I got hit with the "Too many certificates already issued for domain"! I tried revoking the domain in question, but still get the error!
So what now? do I have to wait for 59 days before I can try and get it to work again?!