Not sure why my previous post about this was deleted???
After upgrading to latest version I noticed that the Lets Encrypt certificates no longer work. They were installed from Linux command line. A plugin was not being used.
Any suggestions would be helpful
Your previous post has been deleted because you don't use our LetsEncrypt plugin and therefore, the question is not really i-MSCP related.
When running certbot manually (out of i-MSCP context), the SSL configuration stanza is automatically injected in Apache2 vhost file. However i-MSCP doesn't known nothing about them and so, when you reconfigure i-MSCP, those configuration stanza get lost (expected behavior since i-MSCP regenerate the vhost files from scratch.
To resume, that is not an i-MSCP issue. If you run certbot manually, you must known what you're doing.