Qubes R4.2.4
I recently got a new computer for using Qubes. I removed the SSD from the old one and put it in the new. Everything started up fine and I was able to use it normally (after running Qubes Update and updating drivers for the new computer). The only issue I am having is I can no longer use USB devices except for the keyboard and mouse (both are USB). The old computer had a sys-usb for managing everything, and it was functioning properly. Now with the new computer, sys-usb is still present and starts, however it does not seem to do anything. When I click on the tray icon in the upper right for Qubes Devices, the only thing showing is the Microphone, there are no USB devices present. I plugged in a device and ran ls-usb in dom0 and it found it. The Global Config page for USB devices shows the following message: “Unexpected policy file contents: No USB qubes found: to apply policy to USB input devices, connect your USB controller to a dedicated USB qube.” I followed the steps here USB qubes | Qubes OS to remove the sys-usb qube (grub 2) and rebooted. The same issue persists. I have not wanted to mess around too much on my own for fear of doing something to brick the system, but I did see that in /etc/qubes-rpc/policy/qubes.InputKeyboard it shows $anyvm $anyvm deny (on a single line). Should I change this to “allow”, or is there something else I need to do? Any help would be greatly appreciated.
Check the settings of sys-usb, in Devices tab, make sure that the USB controller is attached to the VM.
See:
Than you. I had tried that already but did not know which controller to attach, which is why I removed to sys-usb qube.I am trying to get back to using qubes without a sys-usb.
Sorry, I dont really understand your actual question 
Are you aware of the security consequences of not using a sys-usb qube?
You should not manually edit a random RPC file like the one you mentioned. Instead, use the Policy editor.
No problem, I rambled a bit in the op and may not have been been clear enough. The issue was that qubes would not “see” any USB devices (except, oddly, the keyboard and mouse, both of which are USB). I had removed the sys-usb qube and rebooted, hoping that would fix the problem. It did not. Just before writing this, I ran sudo qubesctl state.sls qvm.sys-usb and sudo qubesctl state.sls qvm.usb-keyboard in dom0 to recreate sys-usb. After rebooting, sys-usb now functions properly and I can use USB devices like normal. I had tried this once before and it did not work, so I do not know why it worked this time. I knew I had to assign the USB controller to sys-usb, however I did not know which one to use and did not want to try random ones. Apparently this time it found the correct controllers to use. Anyway, it is working now! Thank you!
Do you see anything that could be improved in the docs concerning your issue?
The only thing I could think of would adding a section for moving a SSD (or HDD) to a new computer, if it does not already exist somewhere. If using sys-usb on the old computer, obviously the new computer will have different devices. I would suggest adding instructions for either how to update sys-usb for the new controller(s) or steps for how to remove and reinstall sys-usb to detect and add the correct controllers. Hopefully that made sense!