Actually, yes, the control panel deletes the old certificate files if it detects the domain list has changed before calling certbot to get a new one. I guess I wouldn’t have to do that anymore, but certbot should still not freak out about that and respect the --cert-name parameter when trying to get or renew certificates - even in the rare case that they are broken or no longer exist.
The deletion code I use removes files from these locations
/etc/letsencrypt/live/
/etc/letsencrypt/archive/
I’m assuming if I removed the .conf files in the renewal directory of /etc/letsencrypt/renewal/ as well that would be sufficient to work around this issue? I still think certbot should go with the provided --cert-name parameter no matter what it runs into for storing new certs.