As user_data and chat_data might be changed between updates (e.g. when storing information from background processes that need to be visible to the user on request), they should be updated before calling flush() on shutdown of the bot. I therefore added the method update_persistence() to the Dispatcher class, that is called from the Updater before flushing on shutdown.
Also, since it will be called on shutdown, flush() should always flush. I therefore edited the method in PicklePersistence to be independent of on_flush.