In section 2.4.5 Transform, the specification states that

v. All other properties of the copied nodes are preserved.

The copied node may be a document node.  This means that the document-uri property will be copied.

However, in section 2.1.2 Dynamic Context of XQuery 1.0 it is stated that

"This means that given a document node $N, the result of fn:doc(fn:document-uri($N)) is $N will always be True, unless fn:document-uri($N) is an empty sequence."

The query

  copy $N := doc('data.xml')
   modify ()
   return fn:doc(document-uri($N)) is $N

demonstrates that this is violated.

I would expect that the document-uri property should not be copied, and that document-uri($N) should be the empty sequence.