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The Annotations plugin doesn't back up your annotations - it imports them into a custom column in calibre.
The annotations are stored in a sidecar or companion file on your Kindle. I believe they use the .MBP extension. You would need to copy those files along with the book to keep your annotations intact when adding a book to a Kindle. Calibre doesn't have a mechanism to manage these files, you would have to do it manually.
G
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