I set up a usb qube, I have all usb controllers assigned to it. It is based on Fedora 26. I am on Qubes OS 4 rc5. When I shutdown the Debian 9 TemplateVM all usb devices disappear from the list of attched devices. I then have to restart sys-usb.
I've tested to see if it does it with any other TemplateVMs and it does not, only Debian 9.