Lois did know about the other lois,and that she had come to their universe, but she didn't know about Alt-Clarks's trip there- when he helped lois out when Clark was in trouble. She thought she had only spent a few days in the alt-universe and they hadn't seen each other again. And by the way, didn't Altclark kiss lois in that episode? shock If so, how is clark gonna explain that, especially after not telling her he was there?

Oh and by the way, great story laugh

Anyone can do any amount of work, provided it isn't the work he is supposed to be doing at that moment. ~Robert Benchley