IsolatedStorageSettings ApplicationSettings for Windows Phone 8 Updates
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Isolated Storage Settings provide a convenient way to store user data as key-value pairs in local isolated storage for the lifetime of the application. You can find more details on the IsolatedStorageSettings Class .
So the answer is that the Windows Phone app will keep any data saved after the app was updated. If you uninstall the app, you will lose all your data from IsolStorageSettings.
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