So, what's this 'context' used for? It made me a little bit confusing about the application's life cycle, like we're going to have some 'zombie' application? Thinking about the permissions, we will have runtime permissions stored in the Application instance, and persistent permissions stored in ApplicationData, things would be complicated if we have a unknown status.
I think just destroy the application instance would be simple and clear, or, let the Application instance represent a application no matter it's running or not (have a flag indicating its status).