What happens to the files created by Isolated Storage when the OOB app is removed? Do they remain or are the files also deleted? From what I can deduct the files would be maintained so they can be accessed by the same app in browser. Right?
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Correct, the isolated storage files remain.
End users can remove all isolated storage data, or data for a specific app, through the Silverlight Configuration dialog. It is available both in the Start Menu / Applications menu, or by right-clicking on the plugin.