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Actually you can do both. If you e-mail your books to your Kindle's e-mail address or use the Send to Kindle app, the books will be stored in the Amazon cloud and synced across devices. You cannot sync any books sideloaded via USB.
As for exporting your notes and highlights, they're stored in a "My Clippings.txt" file. You can copy-paste it to your PC from your Kindle.
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