When a pane is closed with the X button, it actually goes hidden. This means that the Pane is still alive as instance in the RadDocking control, but it's not located in the RadPaneGroup.Items collection. You could show the pane (after closing it) using the RadPane.IsHidden property. If you want to remove the Pane completely from the RadDocking control, I would suggest using the RadPane.RemoveFromParent() method.
The pinning/unpinning pane scenario is the same with above - when a pane is unpinned, it's removed from the RadPaneGroup.Items collection and placed inside an AutoHideArea.
Hope this sheds some light on the given scenario. Please do not hesitate to contact us if you have any additional questions.
All the best,
the Telerik team