Filed taxes without 1099 income?

I filed my taxes based only on my w-2 wages. I got a very sizable refund because I got a first time home buyer credit. i just got my 1099 and it is an extra 39k. what am I going to have to do about this. I know I will have to amend my taxes asap but will the IRS come harshly? especially since i likely won't qualify for the Home buyer credit with all of this income total.