How do you let Certbot do it automatically? I would probably like to do that in the future.
Oh, that's a great mess.
As written:
If you try to get a new certificate with the exact same hostnames as in an already existing certificate, certbot should ask you if you want to get a new certificate (not really a good reason for that option by the way, as you already have the certificate) or if you'd want to (re)install it.
However, I'm not sure how certbot handles a certificate which is partly installed already (your .net domain) and partly not installed. If you only have the port 80 virtualhosts for the .com and other domains, it should generate a new -le-ssl.conf file for those.
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