It's normal for the COM port to disappear while the main firmware is being updated. It should reappear about 30 seconds later when the upgrade completes. However, there is some sort of bug in Windows 10 that sometimes causes it to ignore the USB port that a Duet was connected to after a firmware upgrade. When it happens to me I either change to a different port, or if I am using a USB hub, disconnect and reconnect the hub.