State not retained with $href in a webview with native transition

While creating a jason for a web container with native transition as described here things work perfectly fine with android but not on IOS.
The website which I am using for the web container requires user to login to view the website. Now after the user logins he successfully sees the next view but when he clicks on some other link on the page it again asks the user to login after a native transition to the new view which is the issue. Links with just "type": "$default" works well. All the pages which do not require the user to login also works perfectly.
I even tried this with the JASON app for IOS and the issue replicates. Also everything works fine on android so this is an issue with just IOS builds.
On looking further into the issue I found out that Jasonette use WKWebkit to display Web View on IOS devices which does not automatically preserve cookies. You could read a discussion on stack-overflow here.
As I am new to the project I cannot exactly find out a way to fix the issue. If someone could take up this issue or guide me in a direction so that I could push a fix then that would be great.

Regards,
Ronak Shah

Start by tracing the iOS WKWebView flow used for $href links and native transitions, comparing it with the working Android behavior. Reproduce the login flow in the JASON app for iOS and verify that authenticated state is retained when navigating to another page; the linked web documentation and cookie discussion provide context.