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No, you can sync non-Amazon books using the conversion feature in Calibre that puts an ASIN number into the correct field in the Metadata. There are a couple of threads here on how to do it if you look around.
Now no, you can't upload the books to your Amazon account archives. What I, and many others do, is maintain our complete libraries in another online service (see Dropbox below). That way I can download my books to any device via WiFi/3G if that device can connect to the internet. I think you could also use the Calibre Content server for that if you wanted to set it up.
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