I extended some existing certificate with a new subdomain and got:
Congratulations! Your certificate and chain have been saved at /etc/letsencrypt/live/mydomain-0001/fullchain.pem
I am not sure why and if i will get 0002 on the next update, but it breaks the “certificate lies under live/domainname” structure in an unexpected way, especially when it’s not always a folder with a counter.