My experience from firmware update in VMs is that the NK3 is quite robust and most likely in a bootloader mode. Nitropy would detect this and continue the flashing. The bootloader mode looks like it is a different device and Qubes or a VM needs to have that new device also attached.
When running on a different OS and try to experiment with new NK3 releases, I used vagrant to spawn a VM for upgrading. In my configuration are the different USB IDs that are possible.