I started let’s encrypt a few months ago, and my first renewal came up.
the ./letsencrypt-auto renew --dry-run command always came up with one vhost ( i am running three) missing.
When checking apache2, all three were fine.
After a lengthy search, i came up with a post saying that let’s encrypt only supports one vhost per ssl.conf-file (non ssl seems to be fine running all three in one file).
To ensure nobody has that problem, i am posting this. Open your default-ssl.conf - file (or whatever it’s called) in an editor and make one file for every vhost you are running.
Save them, then a2dissite the default-ssl file (e.g. a2dissite default-ssl) and a2ensite your seperate vhost files (e.g. a2ensite your-first-website, a2ensite your-second-website and so on…)
The restart your apache and run the renewal command. worked perfectly fine after that!
Good luck, everybody!