At first install latest Webmin 1.942 and Virtualmin 6.09 GPL.
Afterwards, install certbot package and try re-requesting SSL certificate manually from Virtualmin/SSL Certificate page. In the future, it should automatically request certificates for you.
certbot is only an option on relatively new distributions. OP hasn’t told us what distro/version they have, so it may not be an option for them, but Webmin 1.942 has an updated acme_tiny client, so it can probably still work.