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Hoping not to hijack a thread but this actually helped me with a similar problem but my mail server uses nginx for the webmail options. My auto renew shell was working in July but no more. I changed:
./certbot-auto --config /etc/letsencrypt/configs/my_real_domain.conf certonly (where my_real_domain is replaced with my actual domain)
To:
./letsencrypt-auto renew --nginx and it works now.
Of course I use these same certs in /etc/letsencrypt for dovecot and webmin as well as nginx. This changed way knows where the config file is.
I was dismayed when I opened my email client and got the cert warning. The cron driven update script tried to run on the 1st but it failed and I did not know it. Thanks!
@dwstudeman, the recommended form is just ./certbot-auto renew. All of the other associated information for all certificates should be saved automatically and used for the renewal process.
OK, I see now, ./certbot-auto renew is all I needed on my update script. I tested and it does indeed work without all the other stuff. My original certonly flag probably did not help.