I'm aware of innate (your word actual) conscience, or our innate goodness. I'm not aware of "habitual" conscience. But if I may infer, since you use the word habitual, then it implies conditioning; school, church, political, social, cultural, regional,friends, nationality, and all our acquired biases.
Therefore; Habitual conscience is only a reaction to whatever stimulus we are experiencing at the present moment. While innate conscience is the real us, devoid of dualism, prejudices, preferences, affiliations, etc.