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And you might want to disable, or set to zero, the caltrash bin, otherwise every book you delete will end up cached for a period of time. (in case you change your mind and really wanted to keep the book.)
Right-click on the "Remove Books" icon, and select "Restore recently deleted" and set "Permantly Delete after" to zero.
All those duplicate folders, were they all added into Calibre on the same day? or maybe a small range of dates? (In the edit metadata screen check "Date:")
If they were you could do a search like date:=2024-02-07 for 7 Feb 2024, then simply delete all the listed items.
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