I believe this is a side-effect of switching from a recent release of certbot-auto (or letsencrypt-auto) to the (older) letsencrypt package in Ubuntu 16.04. The older Ubuntu package is not forwards-compatible to configuration files generated by more recent releases. You have a couple of options:
- Continue using
certbot-auto. You can follow the instructions on thecertbothomepage for Ubuntu 14.04 - they work just fine on 16.04. - Start with a new configuration. The cleanest way would probably to do something like
mv /etc/letsencrypt /etc/letsencrypt.oldand then re-issue all certificates. - Try to manually fix the configuration. This is probably tricky and error-prone. The best way to attempt this would probably be to issue a new certificate with the
letsencryptcommand first, and then compare the generated config file in/etc/letsencrypt/renewalwith the one that’s failing at the moment.