I'm by no means an expert on this, but I don;t think it would lose any nutritional value at all. A bit like toasting sesame seeds.
A good way to use flax seeds is to soak them then add them to whatever you are cooking. I personally use them in yoghurt - they soak up fluid from it and seem to lose that bitter flavour.
They tend to go rancid once they have been ground and if I recall correctly lose the Omega's that you want. So best to grind on as needs basis. Another option is getting flaxseed oil and using that with some cooking.
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