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Why is it that people will spend an inordinate amount of effort on the wall and roof insulation and then put big thin, low R value windows in, and wonder why the heat losses are so big? The other issue that must be considered is that the windows will act like large radiant cooling panels in the winter if they aren't high performance units.
What climate zone are you in? You can't alter the laws of physics, if you've input the envelope data correctly and the program sez you need supplemental heat, then, you probably do. I guess it's too late to go back and get better windows?