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I have got some issues with collections too, as i have lost them 2 or 3 times. I have seen it occur when the device resets after trying to open an lrf created from a web page, and i think it happened also after adding some books with calibre and unplugging the usb cable without safely removing the device (though i am sure all transfers were finished before doing that). After collections were lost, recopying books from calibre did not fix the issue, and i had to format the sd card and the internal memory to get them to work again.
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