I'm having the same issue of this fellow user. I have a certificate stored in the Windows user personal store and in a YubiKey. When I plug the YubiKey, the Certificate Propagation Service discovers the certificates in the PIV applet and add them in the personal store using this parameter: CERT_STORE_ADD_REPLACE_EXISTING_INHERIT_PROPERTIES
In this case the certificate in the personal store will be updated, private key will be striped and the certificate will be linked to the smart card.
The solution proposed is to disable the Certificate Propagation Service. This method will solve the problem, but the side effect is that it disable the certificate discovery for every smart card plugged in to the system. De facto rendering all smart card not Plug and Play.
Is it possible to configure the Certificate Propagation Service with a filter that ignore specific certificates? For example, a specific certificate thumbprint.
If this is not possibile, is there a way to manually install a smart card certificate into the personal store, without using the Propagation Service? I know that some smartcard middleware allow this type of operation. I don't know if something similar is possibile using the YubiKey minidriver/software.
