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They're stored in the sidecar folder in a file with a ".mbp" extension. If you delete the book, this file will also be deleted. However, notes and highlights are also stored in the "Clippings.txt" file, and they don't get deleted from there. Copy the sidecar folder to your PC before you delete the book, and copy it back again when you put the book back again, and you'll preserve everything.
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