When a checked item is programatically removed from the RadTreeView.Items collection, it isn't removed from the CheckedItems collection.

Edit: Please avoid using this collection because it has never been implemented completely in RadTreeView. In DataBinding scenarios, you can use CheckBox in the ItemTemplate of the RadTreeView. Approach can be found here =>
http://docs.telerik.com/devtools/wpf/controls/radtreeview/how-to/howto-tri-state-mvvm.html 
CheckedItems colelction can be implemented in the ViewModels, instead of using the built-in property.

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.