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One note on caution about the Amazon system is that it tends to work much better with the books purchased on Amazon than with those that are side-loaded. For those, highlights and annotations are sync'd, backed up and accessible both with the website and in a text document sitting on your device.
But things are not as smooth for side-loaded content.
For example, if you 'drag and drop' a book onto your kindle, it will not sync annotations.
But you can email books to yourself, thus adding the documents to Amazon's cloud. The documents you add like that will be sync'd across devices - and highlights and annotations will be seamlessly backed up. But, for some truly annoying reason, those annotations will not appear on Amazon.kindle.com. Which frustrates the heck out of me.
Unless I am doing something wrong. I have been busy lately and have stopped worrying about this (after struggling myself with SONY's system first for a while - but that was before Evernote).
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