The CheckedItems  collection is not cleared when ItemsSource is changed.

Please consider CheckedItems as not supported collection in RadTreeView. In DataBinding scenarios , use the approach described in the following article:
http://docs.telerik.com/devtools/wpf/controls/radtreeview/how-to/howto-tri-state-mvvm.html 
This way you will be able to create CheckedItems property in your ViewModels.

The XAML team has recently reviewed this issue and will not be addressing it as at this time the team is focusing on the bugs impacting the highest number of developers. If you have encountered this issue and it is blocking for your work please contact us through the support ticketing system with details on your setup and a reference to this item.