If those 3.3.0 folders have already been renamed then can't you just restore them from backup? And then the cert renewal would continue as before.
I see your webroot-path in the renewal config is a static folder so looks like your server should know where that is regardless of the current app folder being 3.3.0 or 4.0.0 or whatever. I am guessing but looks likely.
You could test that assumption and idea by running one renew like this
sudo certbot renew --dry-run --cert-name h9qkct2hr8.qa.egnyte-appliance.com ... (other options)
The (other options) in that command are whatever you need for ccnfig-dir or any other overrides. You would point those at your 3.3.0 as you have been.
If that all works you then develop a way to copy the cert files you need (usually just fullchain.pem and privkey.pem) from the 3.3.0 folders to the new location. And then work on a more permanent solution later.
You have a poorly constructed system of some scale. There are tradeoffs in all options. Really all we can do is suggest ideas and inform some technical details of Certbot. Only you have the full picture of your system and how you want to manage it. There are often many good ways to manage such a problem.
You may want to consider hiring someone with specialized expertise. If @schoen is available he could work you through it. He used to be on the Certbot dev team.