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gaga55, I don't know why storing books in subdirectories or on an SD card would trigger these problems, but for me, they certainly do roughly coincide with recently starting to load my books onto an SD card with calibre, rather than dropping them directly into main memory!
PeterT, I can make a database dump available to you if you will point me to instructions on how to do it. I take it that scrutiny of the config file and epub didn't reveal anything.
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