Issues with Nginx Let's Encrypt Certificate

I'm not sure how this Community can help. While we regularly help people with Certbot, those cases one usually runs Certbot manually. However, with NPM in play, it's rather a "black box" on how NPM installs, manages and uses Certbot. And to me this problem has everything to do with how NPM installed Certbot and you're probably best of asking for help at the NPM support channels. It might be a bug on their end.