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I don't know if this helps or is relevant, but it seems that sometimes it takes a while for your annotations to be loaded back into a book (at least on the iPad). I downloaded and opened a couple of books yesterday that I'd previously finished reading some months back, and initially the annotations did not appear. I thought they were gone. But when I checked some time later, they had appeared. In one case, I had to remove and reload a book a couple of times before the annotations came back, but I can't be sure if this is what made the difference.
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