(Nitrokey 3 - Linux)
Each functionality of the Nitrokey 3 can be reset individually.
The Factory Reset operation deletes all (and generates new) secret FIDO2 keys stored in the Nitrokey:
nitropy fido2 reset(execution requires Administrator rights)
Google Chrome: Manage security keys via the direct link: chrome://settings/securityKeys
Static passwords and One-Time Passwords (OTP) can be reset with
nitropy nk3 secrets reset.
The OpenPGP Card can be reset with GnuPG:
gpg --card-edit, then