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Annotations are stored in a sidecar folder on the Kindle Drive, located at {book-name}_{ASIN}.sdr (versus the same name but ending with .azw(3) for the book itself). All you are transferring is the .azw(3), which is why you don't have any annotations.
The only way to get them is from the account that owns the book, by downloading it through your Kindle, via WiFi. Once there, they are just files on your Kindle.
As nynaevelan said, you cannot transfer them between accounts.
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