It sounds to me that you require two different copies of the apps config files (where in Evince's case is where it stores the list of recent files) rather than two copies of the app itself. I'm not sure if there's a generic way to do that that would work for all apps. You would probably need to modify the app's source code.

More likely, you would need to make a suggestion to the app's author giving as much details as possible for your desired use-case, as there may be other ways to implement what you want.