I have the same issue with Ubuntu for my T430 NitroPad and never made it back again as good as it was with the preconfigured Qubes. I gave it up sometime ago. Last chance is to ask NitroKey customer support as they should know how to setup things correctly.
Right, Qubes was a fun experiment, but it’s just too bad for performance. I actually received a reply on the original post on how to reset the setup. Then you can just keep the NitroKey in the laptop all the time and it will be smooth. However, I think I messed up the partitions and thus couldn’t use factory reset. Whatever the case, I gave it away recently.