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I'd suggest letting the device communication job finish. You can't expect anything to show up in the "On Device" column unless Calibre has finished indexing what's on the Kindle.
That said, I don't own a Kindle, so I can't say how long it normally takes for that. One thing you can do, though: If you have PDFs loaded on your device, try to disable the pdf metadata reader plugin (see preferences->plugins)- some of the time, PDF metadata reading or writing gets hung up on a file.
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