Version 1.3 (recently released) addresses the request in this thread with a new Paste Special | Copy (also the default Ctrl+Shift+V behaviour instead of Duplicate) that functions.
Paste Special | Duplicate functions the same as before (other than no longer being the Ctrl+Shift+V default), which only preserves logical links in the data being copied (existing logical links to non-copied data are not preserved, but those underlying items are duplicated).
The new Paste Special | Copy preserves existing logical links to data not being copied as well as logical links in the copied items.
Here is an example:
Root Item
-+Child A
-+Child B
--+Child C
----+Child D (logically linked)
--+Child D (logically linked)
---+Child A (logically linked)
-+Child E
Child B is copied to the clipboard, then Child E is selected
-- if Paste Special | Copy is used, Child D will remain logically linked, and Child A will remain logically linked (to the root)
-- if Paste Special | Duplicate is used, Child D will remain logically linked, but Child A will be duplicated under the new Child B
Hope that is clear...
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