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Sometimes mine takes a long time too, even in a wall charger. I've had it indexing for up to a month before with less than 10 books for some reason. It seems to confuse it when I plug into my computer. It starts reloading a few sideloaded books, even with Calibre turned off. I don't plug into the computer much but have noticed this because it will mess with my library settings.
I am not sure why yours started reindexing so many books, though. What a pain.
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