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Mine doesn't show this problem, but I would suggest you exit the book you're reading before you connect to the PC. I remember one of the nooks have this issue, the reader would not handle gracefully the media partition being unmounted (so it can be accessed on the PC), and would lose your current page - but that was supposed to be fixed.
Regarding the annotations, I don't use those, but I believe the data is stored internally, so you can't access it.
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