Nginx LetsEncrypt Error

You can inspect all your nginx vhost and config by doing a full nginx config test output (-T) to a file and inspect that nginx-config-test.txt file - I wouldn't share this publicly as it would have sensitive info. Using -T will output contents of all nginx vhosts and nginx.conf and other config files.

Code (Text):

nginx -q -T 2>&1 | tee nginx-config-test.txt

Pay attention to server{} context's listen and server_name directive values to see if there's duplicates or overlaps. You can use command below to do a quick filter for those 2 values as well

Code (Text):

nginx -q -T | egrep -v 'fastcgi_param|server_name_in_redirect|server_names|#|sn=' | egrep -in 'listen|server_name'

example on fresh Centmin Mod install with no vhosts added defaults

Code (Text):

nginx -q -T | egrep -v 'fastcgi_param|server_name_in_redirect|server_names|#|sn=' | egrep -in 'listen|server_name'
343:            listen   80;
344:            server_name demodomain.com;
350:            listen   80;
351:            server_name www.demodomain.com;
459:            listen 80 default_server backlog=262140;
460:            server_name mainhostnamedomain;

Note if you have any older nginx vhosts with no mention of listen 80 port and only server_name listed, then absence of listen 80 directive is same as listen 80 set defaults. So if you have 2 nginx vhost configs one with listen 80 and one without and both list server_name value = domain.com, then you'd get duplicate directive warning (not error) as they're essentially the same when non-HTTPS port 80 requests go to domain.com, it would match on both nginx vhosts AFAIK