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I assume you're using the Find Duplicates plugin, it looks at the values in in the calibre library database not the library folder names.
Calibre uses the file system as backing (secondary) storage for it's library database. The folder & file names in a calibre library are 'arbitrary', which approximate to what's in the database (which is what you see in the book list etc) - it is better by far to ignore the author and book folders.
If you change an author or title the library folder and file names will change, in some circumstances including the book number.
BTW in Nether Scroll (5712) you have files that shouldn't be there, see attachment.
BR
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