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Hi Namtar,
With the Kindle, the system automatically sync annotations and highlight between devices, yes. The only req. is that must be an Amazon book. You can side-load mobi books from other stores, but they don't sync, at least, I don't recall they do (I do have several mobi on my Kindle as well)
Also, you should not have any concern about books being deleted. That is unlikely. The only time that such thing happened was because by mistake, a copyrighted book was being sold or something like that. In order to avoid legal issues, Amazon returned the money and deleted the book. I am not saying that was good or bad, but it was more a technical error when uploading or putting on sale the ebook.
Having said that and regardless of the device, I always, always take a backup of my ebooks; they are in 3 different places and not only on my Kindle or Amazon store.
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