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[1] Create an exact copy of your larger Library with a 3d (new) name.
[2] Calibre > Preferences > Adding Books: set your Merge Books and related options when adding a book that already exists (i.e., same Authors and Title) in the current Library.
[3] From the smaller Library, select a sample of books to Copy to Library #3.
[4] Quick Switch to Library #3 and see what happened and what needs to change in your Preferences.
[5] Repeat 2,3,4 until you get the results you wish.
Once you get your Preferences and your procedures the way you like them, recreate a fresh Library #3 (that will become your single "main" Library). Then do a copy of all of the books in the smaller Library to Library #3.
Defragment/Compress #3 using Library > Library Maintenance > Check Library.
As always, keep backups of your original 2 Libraries, and after your 3d Library is complete, back it up also.
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