There is a form 1040-X , amended tax return form for both residents and non-residents to be filled and sent in hard copy. You may need to pay back to IRS as they have returned you more than what you should get.

In fact I am also going to fill 1040-X  for amending my previous returns (in 2006 n 2007),  did the same thing in 2006 n 2007 as yours.

However, do we need to file amended form?? and how will be its impact for green card processing? Anyone have any ideas??