If I understand your scenario correctly your are having:
- Version1 of your application and the users have already saved they settings
- then you change the XAML and other thing on the application and ship Version2.
- your clients automatically loads their saved settings and remove your changes in Version2(expected).
If that is the case the behavior is fully expected as the RadPersistanceFramework saves and loads multiple properties from your UI in order to restore them in their previous state. Based on the provided information you are trying to create some kind of Push notification for your users. You could create an Application logic to lets say store a version variable in an IsolatedStorageFile and check it with the current version of your application. If the previous version of the app is V1 and your are running V2 project it will detect that and you could delete the existing settings or simply save them without loading them.
I hope this information helps.
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