You can always generate a new key on the card or upload new keys and replace the old keys. (exactly like you upload the first keys. gpg asks if you want to replace the existing)
Also, with GPG you can just extend the lifetime of your keys if you have the keys only on your card and know that they are not stolen.
You can also reset the whole applet by blocking it (entering pin and puk wrong several times) and then send commands to reset it. That is described here:
https://developers.yubico.com/ykneo-ope ... pplet.html