As I have been using Let’s Encrypt since the beginning, the shut down of the ACME-1 servers to be replaced by the ACME-2 servers break the running installation. As for how to migrate an existing installation.

The certbot-auto should have been updated to a version that supports the new revision of the protocol, however, the existing configuration files still point to the servers speaking the old protocol. Therefore you must manually edit the config files to point to the new servers to continue to obtain certificated.

In /etc/letsencrypt/cli.ini locate the line that says 

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

and change it to

server = https://acme-v02.api.letsencrypt.org/directory

Then, per website in /etc/letsencrypt/renewal there is a website.conf file, in each file, make the same change.
And then certbot-auto should be up and running again.

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