Depending on the versions of various components inside QubesOS this might take multiple tries to work. The great people at QubesOS have also done a fix for this re-connection issue, you can find the issue here: https://github.com/QubesOS/qubes-issues/issues/8953 At the end you can find instructions on how to update the affected components. We are also working on a solution based on our NitrokeyApp2 so that Nitrokey 3 updates will work more smoothly in the future inside QubesOS.