Since HIPAA is a federal law, the SAFE act can’t repeal it. However HIPAA was never about protecting patients from the government. It’s full of exceptions.
HIPAA was made to protect the privacy of a patient’s medical records. Severe fines were supposed to be levied on those who disclosed patients information without authorization or to persons who were not authorized to receive it. If you or I violate HIPAA, say goodbye to everything you own. If the Government violates HIPAA, no big deal.