I had the same problem when trying to open the app using a deeplink url sent by mail. I couldn't get the app to open. As a workaround I use an extra page(for example native-deeplink.html) in the theme folder to forward the user from the web environment to the app.
<body>
Forwarding to MyApp
<a href="" id="applink">Click here if you are not forwarded to the MyApp application.</a>
<script>
function getQueryString(){
var queryString = window.location.search;
queryString = queryString.substring(1);
queryString = queryString.replace("=", '/');
return queryString;
}
window.location = 'myapp://link/'+getQueryString();
document.getElementById("applink").setAttribute('href', 'myapp://link/'+getQueryString());
</script>
</body>
The make-it-native app has a built-in scheme. Test out your deeplink handler nanoflow in the MiN app by placing a breakpoint there and if that all seems to work, your logic is correct. Then you can make a build using your own scheme and check if your deeplink handler is called.