It's true that having both notebooks with a highlight can be a bit disconcerting however they are different colours. I suppose that that is because the notebook you have right-clicked to delete is not the active notebook.
However I would say that the dialog provides suitable reassurance as it does confirm with you what you are about to delete.
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Exactly. Why having this strange behavior ? A behavior like the one of the files managers (for example Dolphin under Kubuntu or Explorer under Windows) should seem more appropriate : a click on something (left or right) is supposed to UNselect every directory or unselect every file previously selected... To keep a selection is a stress for nothing... To have to keep an eye on the last alert too.
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