When you generate a SSL certificate for an nginx site through the Virtualmin interface for a virtual (sub-)server, the button “Copy to Webmin” incorrectly triggers the “Copy to Usermin” feature.
On the other hand, the Webmin interface to generate the SSL certificate also fails, because it does not allow for generation for nginxhosts (only Apache hosts).
Trick:
Generate the SSL certificate using Let’s Encrypt in Virtualmin for the virtual (sub-)server. Run the following command as root to copy the certificate to Webmin:virtualmin install-service-cert --domain yourdomain.com --service webmin