Lois tells Conner she's seen Clark on red kryptonite and it doesn't turn him into what Conner had become. However, she has never seen Clark under the influence of red kryptonite and retained the memories of what happened. She wasn't in episodes "Red", "Rush", "Exodus", "Exile", "Phoenix" and "Unsafe". She had no memory of her interaction with Clark in "Crimson" and didn't come across him while he was affected in "Upgrade".