Following up here from the related issue Certbot - Certificate Issued from Let’s Encrypt but Live Certificates Pointing At Previous Versions, I’m unable to reproduce this (without manually modifying /etc/letsencrypt).
@Philiiiiiipp, if you didn’t find anything particularly interesting in the logs yourself, would you be willing to share them with me so I can take a look? Certbot currently doesn’t do much to try and help you if you incorrectly modify the files in /etc/letsencrypt, but if Certbot configured the files this way themselves, it’s a serious bug that I’d like to resolve.
Ideally what I’d like is the full contents of /var/log/letsencrypt. The only potentially sensitive values in there are domains, e-mail, and IP addresses. Feel free to redact those as you feel is appropriate. Additionally, you can e-mail them to me directly if you prefer at bmw@eff.org.