For what it’s worth, as of Certbot 0.10, there’s an easy command to delete a certificate lineage:
certbot delete --cert-name example.com
certbot delete --cert-name example.com-0001
and so forth. After renewing and duplicating a certificate, and reconfiguring your software, you can use that command to get rid of the old one. Carefully, of course.
But i don’t know if the delete command is fast, and it may not be worth automating when the whole issue might be solved soon anyway.