You can either select a specific app running on the key or do a full reset:
PS C:\windows\system32> & "C:\Program Files\Nitrokey\Nitropy\nitropy.exe" nk3 factory-reset --help
Command line tool to interact with Nitrokey devices 0.4.47
Usage: nitropy.exe nk3 factory-reset [OPTIONS]
Factory reset all functionality of the device
Options:
-h, --help Show this message and exit.
PS C:\windows\system32> & "C:\Program Files\Nitrokey\Nitropy\nitropy.exe" nk3 factory-reset-app --help
Command line tool to interact with Nitrokey devices 0.4.47
Usage: nitropy.exe nk3 factory-reset-app [OPTIONS]
{fido|opcard|secrets|piv|webcrypt}
Factory reset all functionality of an application
Options:
-h, --help Show this message and exit.
It is a recent feature according to the changelog:
v1.7.0 (2024-04-24)