I remember seeing some information about this before when I started supplementing flax meal in my diet. I remember that flax seed oil cannot be heated but whole flax and flax meal can be. I also remember someone saying that whole flax seed had to be baked for your body to be able to break it down where as meal did not but I never really saw any proof of that.
This page cites studies specifically about flax seeds in baked goods and the resulting levels of omega 3, and there is not a significant effect at normal baking temps. Are flaxseeds still nutritious even after they are heated or baked?
Research studies have shown that the ALA in flaxseeds and the lignan phytonutrients in this food are surprisingly heat stable. For this reason, we believe that it safe to use flaxseeds in baking and still receive substantial amounts of ALA and other nutrients when consuming the flax-containing cooked foods.
Studies testing the amount of omega-3 fat in baked goods indicate no significant breakdown or loss of beneficial fats occurs in baking. For example, in one study, the ALA content of muffins containing 25 grams of flaxseeds was not significantly reduced after baking. Researchers speculate that the omega-3 fats in flaxseed are resistant to heat because they are not isolated but rather are present in a matrix of other compounds that the flaxseeds contain, including the lignan phytonutrients that have antioxidant properties.