Self signed certificate for communication between local Win10 native app and web app

ERR_SSL_CLIENT_AUTH_CERT_NEEDED means the server is asking the browser for a certificate for client authentication.

You've described how you setup server authentication, but not described how you setup client authentication.

Likely you have enabled certificates for client authentication, but have not configured the web app to send the correct client certificate or have not configured the native app to accept the correct client certificate. That's a very open ended topic to be prescriptive without knowing more about your development efforts, but you can confirm if client authentication is enabled by inspecting a packet capture. One description of the handshake is here : https://blogs.technet.microsoft.com/nettracer/2013/12/30/how-it-works-on-the-wire-iis-http-client-certificate-authentication/.

Just an update: I implemented a javascript workaround to get around my communication issues. When first loading the web app, I simply send my first communication to IIS (destined for Win10 native app) in a separate chrome browser tab. For whatever reason this allows for successful acceptance of the certificate and kick starts the communication with IIS. This is my code to send the command in a new tab and then close it:

    var inst = window.open(launchWinAppURL);    if (inst != null) {        window.setTimeout(function() {            inst.close();        }, 1000);    }

This is not the most elegant solution, but it seems to work on all chrome versions, so i'm satisfied.

Is the web app only communicating with the one win10 machine? Have you installed the self-signed cert directly to the machine? I would try installing it directly to the machine and see if the later instances of chrome allow communication.