It doesn't matter where the key is stored. Private key alone is not sufficient to migrate CA, you need to have a certificate as well. Make sure if certificate is installed in Local Machine\Personal store (certlm.msc), then make sure that private key is associated with certificate. You can force key association using certutil:
certutil -csp "SafeNet Key Storage Provider" -repairstore my "<CertSerialNumber>"
where <CertSerialNumber>
is the cert's serial number. If the command succeeds, then you will see a key icon on top of certificate icon in certificate manager.