Ubuntu 16.06 Xenial Certbot Still Using Acmev1 (last package version is certbot version 0.31.0)?

I think _az is correct that there is a reference acme-v01 in the files under /etc/letsencrypt/renewal. The line probably looks like:

server = https://acme-v01.api.letsencrypt.org/directory

Deleting that line from your configuration file should solve the problem.

As for why this happened, I think there was a problem with the ACMEv2 migration we did in Certbot a long time ago for certificates that were initially issued using letsencrypt 0.4.2 or older and have since then only used the renew subcommand to renew your certificates. If that’s what’s going on, it was a bug in Certbot and not due to any misconfiguration on your end. Thanks for using Certbot for such a long time and sorry for the trouble.