Hi!
You need to remove the key’s stub. As far as I see you need to do so by hand, see:
E.g. in my case:
$ gpg2 --delete-secret-key szczepan@nitrokey.com
sec rsa4096/D9BAE35991DE5B22 2016-01-11 Szczepan Zalega <szczepan.zalega@gmail.com>
Delete this key from the keyring? (y/N) y
This is a secret key! - really delete? (y/N) y
### or by hand
$ gpg2 --with-keygrip -k szczepan@nitrokey.com | grep Keygrip
Keygrip = B06F064034E06C022592DF7C411487BFA5E40AAD
Keygrip = F6DA2A42DFCBA0CC25FF281178D8EDB17A648E91
pushd ~/.gnupg/private-keys-v1.d/
mv B06F064034E06C022592DF7C411487BFA5E40AAD* /tmp
mv F6DA2A42DFCBA0CC25FF281178D8EDB17A648E91* /tmp
popd
I agree it would be nice to have it in our documentation. CC @jan
Edit:
Later on just running gpg2 --card-status
will make them recreated.