Installed libnitrokey. Tried to upgrade NK3AM firmware using linux binary (latest version); upgrade failed.
Put the 41-nitrokey.rules file from your docs into /etc/udev/rules.d/.
Retried upgrade of NK3AM firware → success.
This happened because I had upgraded my fedora template and forgot to put the udev rules file into that folder again (fresh template). However, it is my understanding that installing libnitrokey is supposed to also do this.