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Deleting the .dat file too seems to solve it (I tried deleting .bin or .bin and .dat, I didn't tried deleting .dat only).
But the metadata is created in the .bin file, and the .dat is not created until you actually open the book. So I guess the solution is backup your .dat, delete .bin and .dat, browse to all folders to re-create the .bin files, then restore the saved .dat.
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