This is a known issue with 2.0p5 that will be fixed with the next release of the SDK. Basically it's using a sledgehammer to respond to the fact that something was edited and refreshing it. Since the new SDK can communicate with the message bus this is totally unnecessary...
In the meantime you should be able to patch your app by defining a global Rally.getApp function that returns your app instance to prevent the hard refresh:
//In your app definition give it an xtype:
Ext.define('My.App', {
extend: 'Rally.app.App',
//...
alias: 'widget.myapp'
//...
});
//Find the app instance by its xtype and return it
Rally.getApp = function() {
return Ext.ComponentQuery.query('myapp')[0];
};
You can then delete that code once 2.0p6 is released and you upgrade.