In the case of "She's not joking. She's saying it seriously.", what is "it"? Where is the idea that "it" is replacing? "She's saying she's not joking seriously"? Or is it "She's saying it's not a joke, seriously"?
I understand that I have to use "le" here as the lesson is about replacing an idea, but the idea seems so disconnected that I can't nail down what "le" represents, or why "en" would not be just as valid.