The difference between your setup and mine is the USB keyboard and I think that must be why there’s trouble for you. Did you try attaching the Yubikey manually?
I haven’t been able to select ‘sys-usb’ during setup. I guess that’s because I have only 1 controller but I don’t know for sure. My keyboard isn’t USB so I don’t have to worry logging myself out even when none of the USB slots are working because I can still type my password.
I tried Challenge-Response and it looks like it is working because the Yubikey is detected. Unfortunately I seem to run into an old bug that has been associated with Windows, Dropbox and Google services in the past but looks like to be a thing on Linux as well. After adding the Yubikey I get the following error message:
writing the database failed: Database save is already in progress
Eventually I had to shut down the vaultVM because closing doesn’t work without saving. Unfortunately this corrupts the whole database. I tried a few things (even with the challenge-response secret) but that didn’t work either.
I have 2 Qubes setups on 2 SSDs in my laptop and I did that on my testing setup so even when something goes completely wrong it wouldn’t matter much. I did forget that I registered here on my testing setup before my last keepass backup so I guess the best thing is to always backup again before changing anything. But resetting password works fine on this forum…haha.
To cut a long story short, I think there is a bug with keepassXC because this error is mentioned for a few years now without a clear solution.
I think I will try and see if I do encounter this error on a standalone Linux distribution as well.