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Solved.
I tried loading a new book onto my touch yesterday and Calibre complained about some database error. Quick google pointed towards a corrupted database. No idea how that happened, but I performed a factory reset, upgraded the firmware, loaded all my books again and everything is working fine again.
Would like to know how the database got corrupted (I always unmount/eject the kobo before unplugging) to avoid this happening again. Not a major drama, but annoying nonetheless.
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