I recently removed a certificate from every folder in /etc/letsencrypt but I keep getting an error email from an Anacron job every morning that challenge failed for domain. It keeps renewing the deleted certificate.
Since then, I realized that it wasn’t the best idea to get rid of a cert by removing its files from letsencrypt’s folder.
Where does letsencrypt keeps its list of renewable certificates or how can I tell it that don’t renew this domain?
No, the better way to do that would have been using the certbot delete command.
Your issue could be with the Neth config database. Nethserver uses a very non-standard way to handle the certificates, having decided to reinvent the wheel, poorly. Run config show pki and see if the domain in question appears under LetsEncryptDomains.
There’s the problem, then. Best answer is probably to get a new cert for the desired domain(s) through the GUI. If not that, config setprop pki LetsEncryptDomains "" should do the trick.