Thanks to the forum, I used the following procedure on github :
I enrolled my first nitrokey3 with :
systemd-cryptenroll --fido2-device=auto --fido2-with-client-pin=true --fido2-with-user-presence=true /dev/XXX
Now I physically remove my first key, and try to enroll my second key with the same command :
systemd-cryptenroll --fido2-device=auto --fido2-with-client-pin=true --fido2-with-user-presence=true /dev/XXX
If I try to test my two fido2 keys, they open one slot each:
cryptsetup --verbose open --test-passphrase --token-only /dev/nvme0n1p5
However, when I boot, only the first key I enrolled works. The second is not recognized.
Any ideas?