Hi @acdit
I am not going to try to figure out what exactly went tilt, but rather simply skip to the solution …
(Yes, something went tilt in the installation – I always watch closely and confirm that one of the last things is the confirmation that LE has been installed correctly.)
So to solve this simply run the following line:
sudo certbot register --register-unsafely-without-email --agree-tos --config-dir $STORAGE_ROOT/ssl/lets_encrypt
However, you must replace $STORAGE_ROOT with the actual path to your storage which will be /home/user-data unless you are using a unique storage directory — based on your posts I think that I can safely assume that you are not.
Let me know that this works … or not. 