Well, it depends on how many duplicate (numbers) you actually have. If you think you have many, perhaps you should move the contents of your \Library and start with a new database. Then, just "add" your books while pointing to your relocated \Library and be sure to add all formats, including those that have been converted from the original.
I don't know of an easier way to do it.
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There were no database errors, but as mentioned there are some folders with same name but different numbers.
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Note: The problem is not with folders containing the same
name but different numbers - those are just duplicates that can be removed. The problem is with the folders you have with different
titles that contain the same number.