Application data persists over updates; it would only be deleted if the user uninstalled the application. From Accessing app data with the Windows Runtime:
The system manages the data stores for an app, ensuring that they are kept isolated from other apps and other users. The system also preserves the contents of these data stores when the user installs an update to your app and removes the contents of these data stores completely and cleanly when your app is uninstalled.
Given that, you certainly would have access to the current (old) version of their local database, so it would be up to you to build in any migration/upgrade functionality as part of the app.