Edit this file:
/Library/Server/Web/Config/Proxy/apache_serviceproxy.conf
and comment out these 2 lines
Include /Applications/Server.app/Contents/ServerRoot/Library/Server/Web/Config/ProxyServices/CalendarServer/Unsecured.conf
Include /Applications/Server.app/Contents/ServerRoot/Library/Server/Web/Config/ProxyServices/CalendarServer/Secured.conf
restart the web server and .well-known should start working