i did remove...
$ sudo rm -R renewal/michaeljinks.com* live/micaeljinks.com archive/michaeljinks.com
rm: cannot remove 'live/micaeljinks.com': No such file or directory
(and of course the error is just because there was a symlink to a file we removed in the same command)
then:
$ sudo certbot certonly --nginx --dry-run --cert-name michaeljinks.com -d michaeljinks.com
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Simulating a certificate request for michaeljinks.com
The dry run was successful.