I have not yet tried to use nitropy nk3 factory-reset but following
https://docs.nitrokey.com/nitrokey3/windows/reset
https://docs.nitrokey.com/nitrokey3/linux/reset
Just works fine.
TL;DR;
# Reset FIDO2
$ nitropy fido2 reset
# Reset static passwords and OTP
$ nitropy nk3 secrets reset
# To reset OpenPGP-SmartCard
$ gpg --card-edit,
# then enter "admin" and after that "factory-reset"
# Resetting PIV feels and looks kinda hacky
$ opensc-tool \
-s 00:A4:04:00:0B:A000000308000010000100 \
-s 00:20:00:80:08:FFFFFFFFFFFFFFFF \
-s 00:20:00:80:08:FFFFFFFFFFFFFFFF \
-s 00:20:00:80:08:FFFFFFFFFFFFFFFF \
-s 00:FB:00:00
After that ensure that you follow the init process at a minimum set all needed PINs on each module. Each module has its own PIN or even multiple PINs! IIRC you can not configure credentials on FIDO2 if there is no PIN set. Same for PIV.
May I ask why gpa is needed? I only have seen and used gpg --card-edit to interact with the PGP SmartCard of Nitrokey 3 and Yubikey.