@jsha Absolutely, there are 4 files that have the same name in the same folder structure:
/csr/0000_csr-certbot.pem
/csr/0001_csr-certbot.pem
/keys/0000_key-certbot.pem
/keys/0001_key-certbot.pem
One of the servers also has:
/csr/0002_csr-certbot.pem
/keys/0002_key-certbot.pem
which is not duplicated on the other server. If I understand how the auto-update of the certs work then the other server will get this file when it’s up for renewal. Also this list of files will grow over time with auto renewals.
All the other file names that are duplicated are “namespaced” by the domain name in some way. I think that the easiest solution would be to have all potentially duplicated files immediately namespaced with their domain under the /etc/letsencrypt/ folder and only have neutral meta files that relate to the operation of letsencrypt remain in that folder.