_My web server is (include version): _ Apache/2.4.25 (Debian)
The operating system my web server runs on is (include version): Debian 9.7
My hosting provider, if applicable, is: Owned dedicated server
I can login to a root shell on my machine (yes or no, or I don’t know): yes
I’m using a control panel to manage my site (no, or provide the name and version of the control panel): No
The version of my client is (e.g. output of certbot --version or certbot-auto --version if you’re using Certbot): certbot 0.28.0
Since a while ago certbot just stopped displaying the virtual domains and it displays 2 lines of localhosts as I noted above. Typing “certbot certificates” does list all the certificates installed, but for the above stated reason I can’t install new certificates anymore.
For some reason, you've managed to get two Let's Encrypt accounts associated with your certbot. If certbot only has one account, it would have skipped this question. But as you now have two accounts, it asks you to select one of then to use.
So your virtualhosts probably are just fine, just select one of the two accounts. It really doesn't matter if this is a relative simpel server with just a few hostnames and/or certificates. It's more of a large webhoster kind of usage when you want to manage multiple certificates over a few accounts. So I think it doesn't matter which account you chose.
I have no idea how removing one of two accounts influences renewal of already existing certificates which were issued by that account, as the account ID is saved in the renewal configuration.
I think this happened because I am using Webmin on the server and I created a certification for Webmin from the UI, while for all the virtual hosts I created them with Certbot. Does this makes sense?