Find Duplicates Marks the books it regards as duplicates with a push pin on the extreme left. You can Unmark the books you want to keep with Ctrl+M.
When you've Unmarked the books you want to keep, use the Mark Books->Show Marked Books option, select all the books and remove them via the Remove Books tool.
You might want to add the Mark Books tool to a toolbar or menu. I have it in the book list context menu, and I have assigned custom shortcuts to some actions.
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