@alex,
After install Nginx, CWP will set Nginx to listen to port 80 and forward to 8181, listened by Apache there. By default the installation of Letsencrypt will get Apache also listen to port 443. Therefore one would need to change Apache conf and Nginx conf, in order to make Nginx forward https connection on port 443 to Apache.
I am happy your website will run under https and Nginx. Does your conf survived after Letsencrypt daily certificate renewal? Is your https header responded by Apache or Nginx? (or maybe even Mod Security?) Can you share how to do it? Thanks alot!
pp :> curl -X HEAD -i http://www.my.domain
HTTP/1.1 200 OK
Server: nginx/1.10.3
.....
pp :> curl -X HEAD -i https://www.my.domain
HTTP/1.1 200 OK
Server: Apache/2.4.25 (Unix) OpenSSL/1.0.1e-fips
...