All good and beautiful, however, I've received an expiration notice for the first certificate (the one with 3 alternative names), so, does that mean that the certificate (the old one) is still valid even when the subdomains were added to the new certificate as well?
If so, it means the same subdomain can exist as a subject alternative name in more than one certificate?
You can't add anything to a certificate, nor can you take anything away or change anything--once issued, they're immutable. You issued a new certificate containing more names than the old one. And because of the way certbot operates, it treats the new cert as having superseded the old one, which seems to be what you intended--but the old one is nonetheless about to expire. If the new cert is working fine, you don't need to take any action.
There's no limit (other than the Let's Encrypt rate limits) to how many certificates can contain a given FQDN.
