I had a site called abcd.nexxai.dev and the owner finally bought abcd.com so I went into the site's settings, and updated the root domain as necessary.

In doing this, 2 bad things happened:

1. Ploi didn't automatically suggest requesting a new SSL cert for the new domain
2. It did not update all of the paths in the /etc/nginx/ploi/abcd.com/before/abcd.com file as I would have expected (this happened yesterday so my memory is a bit hazy, but I believe it was the root and include directives)

This meant that not only was the single site's config broken (because they were pointing to now-missing paths on the disk), all of the other NGINX sites on that box went down too because NGINX couldn't restart due to a broken config.