If you are not creating your custom panes dynamically (they are defined in XAML), the easiest fix for this problem is to set the RadDocking.SerializationTag attached property to the pane. Unfortunately if you are adding this kind of panes dynamically this will not help for all cases. In this situation you will need to handle the ElementLoading event of the Docking control and to use the SetAffectedElement method of its arguments to point the instance you want to use when loading. Please, refer to the following code sample that demonstrates how to do that.
sender, Telerik.Windows.Controls.LayoutSerializationLoadingEventArgs e)
Hope this helps.
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