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Are you sure that your Goodreads account isn't linked to your Amazon account? Because the annotations you see are supposed to be from people you follow there and on Amazon who have either shared them from the device / app or made them public on Goodreads, as far as I know.
The "popular highlights" feature is separate, as that shows the most popular passages highlighted in Kindle books by all users.
Both of these can be turned off in Reading Options so that you don't see them (should they turn back up). Since they weren't there when you re-downloaded the book, it may have just been a glitch where the app loaded it without acknowledging your settings.
My highlights and annotations show up on my Goodreads account but they are private by default unless I choose to share them directly or make them public later.
If you're certain that your Goodreads account isn't linked to Amazon (you can verify by going to Goodreads > Account Settings > Apps) then I'd contact Amazon and make them aware of it.
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