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If I were to guess I'd say amazon is detecting that the azw3 file was altered by non amazon tools and deliberately disabling the sync. They imagine they can get away with this because azw3 is a "new" format. They did something similar with .apnx files a while back. Similarly, they deliberately changed the way that their newer firmware loads covers from mobi files to try to force side-loaded books into the "Personal docs" ghetto.
As I said, feel free to experiment, if you find some header field that can be modified to do the trick, let us know.
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