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It kinda sucks but you can only sync books bought/downloaded directly from amazon. Everything else must be synced manually. I think it should be possible to copy annotations to the kindle from your app. Try creating one annotation in the book you have on the kindle, then check the mbp file via usb. There should be an annotation in there, which you can probably copy over with your annotations. I'd guess that the id the kindle uses for files is different to the kindle for mac program. I'm not sure why though, it makes no sense.
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