"renew" does not work with apache and multiple domains (and certonly also not)

You should be able to post more links now.

Sounds quite similar to this issue where it turned out that a buggy cronjob ran too frequently, exhausting the rate limits. You'll probably need to wait a while before you're able to try this again (that post suggests up to a week).

In the meantime, the following things might help us find the problem:

  • Log files from /var/log/letsencrypt
  • Renewal config files, stored in /etc/letsencrypt/renewal
  • Your apache VirtualHost files (usually in /etc/apache2/sites-enabled/)