There's a couple ways you can mingle a native app and a browser app.
Alternatively, rethink your architecture. Have both the native application and the browser based application use the server as a go-between. So both the browser and native application only talk to the web server, which forwards information between the two as necessary.
Or if you need native functionality... just make a single native application.
I do not recommend the 'local web server' approach for anything other than applications run in controlled environments. If your software is intended to install and run on end user machines with minimal support requirements, you'll find yourself dealing with a whole host of firewall and anti-virus software related problems.