What if you disconnect/connect mouse cable when it’s not working after Qubes OS boot up without restarting sys-usb?
Will it be recognized?
You can check the log in sys-usb terminal using sudo journalctl -b command and the log in dom0 using the same command to see how your mouse is handled in sys-usb at boot up and compare it with how it’s handled after disconnect/connect if it works after this. Check in dom0 whether there is a request from sys-usb to pass the mouse input or not.