Yours was without a USB connection.
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That it happened last night without even being plugged in means Calibre and my PC aren't to blame either.
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So Flash storage failed by itself.
The other people are discussing USB transfers, where some have no issues and others can avoid it with a reboot. Definitely SQLight files open.
Your symptoms and solution are different.
Flash storage does suffer from blocks fading even when not in use. An update re-writing files will cure that and absolutely bad blocks will be hidden.