This semantic inquiry is pretty trivial. They mean different things and carry different degrees of importance to different people. Who cares if they're the same or not? When reading advice, you shouldn't take the words literally, but rather come up with your own interpretation. My interpretation of this type of advice boils down to: 'When faced with a decision, think about it [your emotions and instincts come into play here] and do what you feel is right.'
P.S. As an aside: My personal interpretation paints them as fairly distinct, though related, things: Instinct tells you what you should do, Emotion tells you how you feel. They sometimes feed one another (i.e. You see a pretty girl and emotionally fall head over heels which makes your instinct tells you to do something before this angel walks out of your life forever) and sometimes are in conflict with one another (i.e. Your instinct tells you to sell your company because you've subconsciously crunched the numbers and outcomes and decided it's for the best, but you can't emotionally bear the thought of living another day without the baby you've worked so hard on).
P.S. As an aside: My personal interpretation paints them as fairly distinct, though related, things: Instinct tells you what you should do, Emotion tells you how you feel. They sometimes feed one another (i.e. You see a pretty girl and emotionally fall head over heels which makes your instinct tells you to do something before this angel walks out of your life forever) and sometimes are in conflict with one another (i.e. Your instinct tells you to sell your company because you've subconsciously crunched the numbers and outcomes and decided it's for the best, but you can't emotionally bear the thought of living another day without the baby you've worked so hard on).