I liked how Lois figured it out from all the dropped clues in Smallville.
At first, I wondered who her 'source' was in Metropolis and what she had asked him/her, but then I realized she was just checking on Superman's actions. She could've been talking to anyone in Metropolis for that information. Thanks for giving Lois back all HER super investigative powers in this story.
So, the payback is letting Clark know that she knows, or stressing him out that B39 could still be out to get him?