Here is an idea. The 2 versions are a time loop. The Donner Cut happens in which he turns back time and than events repeat themselves slightly differently in the Lester Cut. Think the TNG episode Cause and Effect. There is a sense of Deja Vu but not complete memories. In Donner's Cut Lois seems to have a vague sense of something happened at the end. Perhaps Superman's memories are only partial. He tries going to his mother for approval the second time. He finally excepts things as they are.
I long had the theory that Lois just plays along with the "magic kiss " thing. Knowing its the only way they can move on. When its revisited in Superman IV this was hinted at. When he reveals his secret she has total recall of Superman II but seemingly he does it again. BUT later when she is worried that Superman died she shows up at Clark's apartment. She pores her heart out explaining how much she cares about Superman and before she leaves she tosses Clark the cape! As a kid I never fully understood that. But its clear that she knows and that he knows she knows.