Comment 4 for bug 1628168

I'm confused, you are saying that "All devices seem to be claimed by pci-stub", but looking at the qemu command line, it is using vfio-pci driver (pci-stub is legacy). So make sure your device is using the right driver when it is passthrough to the guest (for e.g. /sys/bus/pci/devices/0000\:89\:00.0/driver should point to vfio-pci). Based on qemu command line, looks like your fine, but just need to validate ...

When you delete the guest, libvirt should reset the driver back. So in my case (I'm using Intel NICs), the driver gets back to ixgbe (I'm using an Intel NIC ). That might validate if the issue is with libvirt (like you are mentionning above).

Also, look at the libvirt (/var/log/libvirt/libvirtd.log) and qemu logs (under /var/log/libvirt/qemu/), there might be something of interest there.