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Reporting back, somehow I still believe it had to do with the character encoding. I closed Calibre since library was unresponsive and when I launched it back, those books with the character encoding problems had lost the metadata but were there ... not sure if there is a way to track what happened from within calibre. Maybe it has to do with the filesystem on the raid (I have had problems with filename encodings from time to time) but it's strange that the files are there but the metadata isn't...
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