Redirect all requests to HTTPS, except for one subdirectory

Try this:

server {
    listen  80;     
    server_name     sub.domain.tld;
    server_tokens   off;

    root /var/www/letsencrypt;

    location /.well-known {
        try_files $uri $uri/ =404;
    }

    location / {
        return 301 https://$host$request_uri;
    }
}

Since there was no try_files entry in your virtual server, it didn't know what to do with requests coming to /.well-known.

Redirect all requests to HTTPS, except for one subdirectory

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