If end-users accidentally or intentionally delete SSL certificate files in the file structure without prior disabling SSL certificate feature through Virtualmin's UI, then it will always give the
Problems with SSL "certificate authority file is not valid" after updating error message as discussed onhttps://www.virtualmin.com/node/54897. And you can't re-enable SSL certificate unless manually go to /etc/webmin/virtual-server/domains/$domain_id file and clean up the SSL certificate-related entries.
And it's not easy to troubleshoot this for non-experienced Virtualmin user. So I believe Virtualmin could automatize the cleaning up process on, for example, check configuration. But ideally this kind of fixes should be offered with additional "Fix found issues" button after Domain Validation process.