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I believe duplicates will be removed when you copy books to a new library. Just create a new library with the switch/create menu on the library button, then select all book and right-click copy them all to the new library (with the appropriate setting for handling duplicates ...).
If there only a few duplicates, manual merging may be faster (Select the one with good title + cover, ctrl-select duplicate(s), then merge via right-mouse menu or shortcut-key "m".
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