This list of names is very long. Apart from nv.twr.cz I think you can safely remove also the names for nextcloud, collabora and mattermost because they are web applications, they define an HTTP route, and their names do not be to be requested also from TLS certificates page with Let’s Encrypt.
If Let’s Encrypt requirements are met for all of those names, manually delete redundant entries from the Traefik’s configuration with a simple text editor, e.g.:
runagent -m traefik1 vi configs/_default_cert.yml