Update:
1. I just downgraded to Calibre 5.40, and the problem persists. Uploading epub documents to my device seems to work fine and finished normally, but no documents appear on the device, nor do they show up in the Calibre library main window as on device.
2. One peculiarity that I neglected to mention: when one of these upload jobs that doesn't actually upload finishes, all the books selected for upload are still selected, except one of them...seemingly chosen at random.
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