Did you select the option to install sys-usb during Initial setup?
This would remove all USB controllers from dom0 and attach them to sys-usb VM.
Since your dom0 need to have access to the USB disk from which Qubes OS is booting it’ll fail to boot when the USB controller will be detached from it.
Disable sys-usb autostart:
And remove rd.qubes.hide_all_usb and usbcore.authorized_default=0 kernel options as well from GRUB entry:
Qubes 4.1 only: You should also add the usbcore.authorized_default=0 option, which prevents the initialization of non-input devices. (Qubes ships with a USBGuard configuration that allows only input devices when usbcore.authorized_default=0 is set.)
If you have only one USB controller then you won’t be able to use sys-usb and you need to remove it:
USB qubes | Qubes OS
If you have multiple USB controllers then you can leave one USB controller that will have your USB drive connected to it in dom0 and attach the other USB controllers for sys-usb:
- Find the controller used for your USB disk.
- Remove the USB controller that is used for your USB disk from the list of PCI devices attached to sys-usb in its Settings → Devices tab (move it from the right column to the left column).
- Open the file
/etc/default/grubin dom0. - Find and remove
rd.qubes.hide_all_usbandusbcore.authorized_default=0options. - Find the line that begins with
GRUB_CMDLINE_LINUX. - Add
rd.qubes.hide_pci=<BDF1>,<BDF2>to that line, where<BDF1>and<BDF2>are the USB controller identifier for USB controllers excluding the one which has your USB disk connected. You can add mode BDFs or less BDFs according to the number of USB controllers that you have. - Save and close the file.
- Run the command
grub2-mkconfig -o /boot/grub2/grub.cfgin dom0.