What I think you mean ( and correct me if I'm wrong ) is that heat may deactivate or reduce the nutritional value of the egg yolk. I have no idea how this translates into needing to store them separate in the refrigerator though? Basically store the egg as a whole and seperate them at time of use is your very best solution...you can eat the yolks raw if you like. The whites contain avidin which deactivates biotin (found in the yolk) if eaten raw. Cooking the white deactivates the avidin which allows better asymilation of the biotin. So sunny side up sounds best to me.