Dear Ali,
All transcripts are evaluated in the admissions process, so your exceptional performance in your first two years will be noted along with your excellent performance in your last 2+ years. How the GPA is calculated depends on the school to some degree, but also how you report it on your application. Most schools will ask for not only a cumulative, but also your GPA for each year, so you can choose to calculate your own cumulative combining all 4+ years of your studies. However, some would say you want your reported cumulative to match what is on your transcript for when you graduated. So, you will have to decide how you want to report--perhaps a good question for the HBS admissions folks at a forum or campus visit? Regardless, I think your GPA is strong and will be more of an advantage than a disadvantage for your future application.
Good luck,
Lisa