Okay, I suppose that your application is hosted on one of your websites. If that's right, when you make an update,you will have to edit the index.html, or the page where the game is ebedded.
Find this line <script src="c2runtime.js"></script> (it calls the game runtime), and change it to: <script src="c2runtime.js?version=x"></script>
where x it's the version of the game, the browser will know that you have a newer version of the code, and will flush the chace memory and get the current script.