I've just read something interesting
about the way that Windows handles private keys for certificates when you delete a certificate. It keeps the private key in a way that if you install the certificate (yes, the public key only) again later, it will allow you to use the private key (that was kept somewhere [Protected Storage?] in the system). So, if you really want to delete a private key for a certificate in Windows, there is a tool to do that in the link above.
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