How to set up HTTP-based domain validation on nginx (how to reroute specifically one url to a text file)

I am having trouble redirecting properly.

server {
        listen 80;
        server_name www.website.com website.com;

        location /.well-known/pki-validation/HASHHASH.txt {
           root /var/www/comodo;
        }
}

does not seem to work (can't find it). Any advice very much appreciated.

With HASHHASH.txt in /var/www/comodo

The root directive constructs the pathname by concatenation, so the configuration in your question expects the file to be located at /var/www/comodo/.well-known/pki-validation/HASHHASH.txt.

You can use the alias directive:

location = /.well-known/pki-validation/HASHHASH.txt {
    alias /var/www/comodo/HASHHASH.txt;
}

See this document for details.

You need to put "" in the link:

location = "/.well-known/pki-validation/HASHHASH.txt" {
    alias /var/www/comodo/HASHHASH.txt;
}