Let's Encrypt creates new config files

The cron job command is test -x /usr/bin/certbot -a \! -d /run/systemd/system && perl -e 'sleep int(rand(43200))' && certbot -q renew.

I do not run an own certbot aside from the certbot that has been configured by / in Virtualmin. I only use the certbot tool to query information and to remove obsolent configs etc.