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Sorry for the late response, but thanks. I ended up using the previous versions for the library, but now I know what to do in case it happens again. The only question I have about this is when I add an .opf or cover file to a book in auto-merge, does it cause the book file to indicate that the .opf file is another book? Or will clicking it in the edit metadata field make it go back to being a file and not a book? ie. adding an .opf file to a folder with an .epub will show that book as being in the .opf and .epub formats.
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