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The list of books shown by Calibre is actually constructed from information in metadata.db, not from the books in the library. Typically metadata.db contains updated metadata while the books still have old metadata. Metadata inside books is normally only updated to match metadata.db when you send books to device, convert them or save to disk. So you have to backup both metadata.db and all the folders in the library. Just copy the whole library folder as a single entity. And restore it the same way.
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