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The way to think about this is that there are two connections present; one is an physical one, the USB cable; the second one is a disk drive that runs over the cable.
The Kobo detects the presence of the physical connection to display the "Connected & Charging" message. Windows detects the disk drive running over the cable.
When you "eject" the Kobo, either from Windows System Tray or Calibre, all you are doing is telling Windows to flush any cache it has, and to disconnect the logical drive; it is NOT doing anything to the physical connection; that will stay active (and charging the Kobo) until you disconnect it.
When the Kobo detects the physical cable as being disconnected, then it will scan for new content and update it's database.
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