Wait, no!
I meant in Virtualmin. Using certbot directly will break things (and maybe why things are broken, if you used certbot for domains that has previously gotten certificates using Virtualmin. You can use either certbot directly or Virtualmin, but you can’t mix and match. And, if you use certbot directly, you need to manually make the files available to all the services, the lack of which seems to be why everything is broken now.
You originally set it up with Virtualmin (we can tell because of the paths), so you shouldn’t change how you’re issuing certs.