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There's no alternative when you have multiple SANs, all of them have to be validated. But since they are free and easy to automate you can just issue a certificate for every domain.

when you remove a subdomain from your webserver and then it refuses to renew them for the entire domain

Most Let's Encrypt clients have the ability to automatically exclude any subdomains that have stopped working. However they don't enable this by default because they have no way of knowing if the domain is really gone or if a janitor just happened to unplug the server to plug in their vacuum when the renewal was attempted.

You should post on the community forum if you ever experience an issue like that again. Https://community.letsencrypt.org

thanks. it was actually my fault, i shouldn't have deleted the virtualhost. but when you have many domains these things can happen