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The specification of the transform copy clause does not specify explicitly what the parent property of the "top" copied node will be. My assumption is that it will be empty. If this is the case, I suggest to clarify this in the spec. Currently, the spec says (in 2.4.5, 1c) "A new copy is made of $node and all nodes that have $node as an ancestor, collectively referred to as copied nodes. Each copied node receives a new node identity. The parent, children, and attributes properties of the copied nodes are set so as to preserve their inter-node relationships." I would add a sentence like: "The parent property of the copy of $node is set to empty"
The XML Query WG, at its meeting today, agreed to make the change that you have suggested.