I have a Yubikey with my GPG private keys on it, and public keys in my gpg keyring. I made sure that private keys are not present on my system by running gpg --export-secret-key -a <key id> which returned nothing but gpg --export -a <key id> printed my public key.
Next after setting up my <key id> for signing I noticed that I still get a private key printed on --export-secret-key after unlocking my card and using it to sign something.
This baffled me because I wasn't expecting anything to be printed on --export-secret-key so I am curious what this key is?
To be sure I have also tried deleting this private key --delete-secret-keys <key id> but using the smartcard again, populates the private key for this <key id>.
gpgconf --kill gpg-agentchange anything?