You can delete files from /etc/letsencrypt/{csr,keys}/ at any time. They are there for archival purposes.
Don't touch anything inside /etc/letsencrypt/{live,archive}/, these are the certificates that Certbot is actively managing. If you wish to delete one of your certificates, you can do so with:
certbot delete --cert-name NAME
where NAME matches the directory name within /etc/letsencrypt/live/. That will delete the certificate from both the live and archive directories.