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Just add (Bulk Metadata Edit) a unique (relevant?)Tag, the Select all : right-click: Copy to Library: <target>:<choice if to delete or not> (Why not Keep, the archive the old lib
Repeat sequence for the other (be sure to use a different tag).
Create VL's by those tags (and whatever).
Copy to Library Moves all metadata and books.
BTW Prefferences :adding Books: Adding Actions has a setting for what to do if it runs into a clash
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