UPDATE
The issue appears to have been my iPhone which was attached (for charging only). Once I removed it and restarted Calibre, it was able to communicate. This issue however happened only when I updated Calibre to 1.50, and not previously. I have set Calibre to ignore all iDevices.
Even though Calibre was not communicating with the Aura HD, the device was still being detected both by Calibre as well as the OS, and I was able use Calibre to eject/unmount the Aura safely. Only the database (which books are on the device) was not being updated when my iPhone was attached.
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