No, sounds logical to me.
If the metadatafile is in /mnt/sd/.Books and it says the book is located at ".Books/Doyle, Arthur Conan/Arthur Conan Doyle - The Adventures of Sherlock Holmes.epub" it will search for "/mnt/sd/.Books/.Books/Doyle, Arthur Conan/Arthur Conan Doyle - The Adventures of Sherlock Holmes.epub". (twice .books)
Did you change the location of the metadata file? Because that will simply not work.
If not, how exactly did you export the books from Calibre? Maybe there is one setting that I have to take into account, since Calibre is able to find the Sherlock Holmes book although the relative path to it does not exist under mnt/sd/.Books
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