If your nginx conf is on for example /etc/nginx/ you could try to search for return or rewrite directives (if it is on another path change it on below command):
I uninstalled the Let’s Encrypt package from my server and deleted its folder.
Then installed it all over again, SSL works fine.
The only sad thing is I won’t be able to know what actually happened since searching for the return or rewrite directive didn’t turn up something that looked erroneous.