Instead of creating a new thread, I have decided to continue over here as this also pertains to renewal and configuration.
One of our domains is throwing the following error,
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/certbot/renewal.py", line 64, in _reconstitute
renewal_candidate = storage.RenewableCert(full_path, config)
File "/usr/lib/python3/dist-packages/certbot/storage.py", line 420, in init
"file reference".format(self.configfile))
certbot.errors.CertStorageError: renewal config file {} is missing a required file reference
Renewal configuration file /etc/letsencrypt/renewal/comedaddymummy.com.conf is broken. Skipping.
This site was fully functional until recently when we upgraded the system and then, tried to set a permanent redirect from http to https using the control panel of the interface used to manage this domain. Since then, the domain is showing the default page, though there is a sym link to the interface, which should show up. When I did a dry run, I noticed this error, which confirms that the issue pertains to the conf file set up after the permanent redirect debacle.
Any thought on how to fix this issue. I noticed a similar thread here, which led me to reach out again.