Changing to the USB2 port is probably the solution. Using USB3 seems to be a problem with the newer Kobo devices. It isn't everyone, and it isn't all the time. But, changing to the USB2 port seems to fix it every time. Or changing to a hub.
How much is the Kobo devices, and how much is the PC or drivers, I don't know. My laptop only has USB3 ports, and I've never had this problem with my Aura ONE.
I do have problem, but it is caused by having loose USB ports on the laptop and the position of the ports. They are in a place where I can bump them partly out. If calibre is processing the device, I'll get an error, but, I don't think it was the one you are seeing. And when this happens, the device is ejected without closing the file system, and it also seems to put the port into strange state. Afterwards, the Kobo devices won't work with the port, and some other devices won't as well. A simple USB memory stick will, but I don't trust it. Other ports are OK. I have to reboot the laptop to get the port working properly again. That sounds like one of the things you are seeing.
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