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I believe that happened to me awhile back and I ended up rebooting the Mac (mine is an older not upgradable Mac Pro desktop still on El Capitan). It was a USB error where the Kindle wasn't mounted as a drive, so Calibre had no idea it was there.
I rarely shut down my Mac so it can go a long time between reboots. It wouldn't hurt to reboot the Kindle at the same time, if you haven't.
Come to think of it, it may have been a Kobo I had the problem with - but the problem was the same and the solution was to reboot the Mac.
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