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As almost suggested, you could also put a portion of your books in a hidden folder, let the rest process, and then move some out of the hidden folder, and process again...
Smaller batches might be more likely to succeed.
I've had to do this a couple of times after database corruption and a factory reset.
Usually database corruption is caused by me being stupid and forgetting to eject before unplugging the usb, but occasionally from some combination of stranger events.
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