From what I understand you have the same application but need to decide which one to use.
Are both deployed in a cluster?
Maybe you can set the EJB "distinct" name for the server's or the application, in that case you have all app's in your outbound connections listed.
But to select an application you modify the lookup instead of the InitialContext.
So you have something like lookup("ejb:my-app/my-ejb/my-distinct/MySessionBean!MyInterface")
Does this is an approach for you?