Could you have converted it when you added it to Calibre? It sounds like you did. Nothing added to your Kindle via Calibre will communicate with Amazon. No syncing, etc. if you just transfer via USB The normal way, it should sync. No page numbers, though. Those don't download with the book when you select download and transfer via USB.
Updates should download to your Kindle if you have autoupdate turned on. I believe it is off by default.
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