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In the quote from Fly Hard that SuperRoo copied from the script, I don't think that Clark made a response to Lois' comment "You're not Superman" in the episode that we saw. Whether or not it was filmed and edited out, I don't know.
I don't know about the script, but he did answer her in the ep. I just watched that part to be sure:

Lois: Clark, take it easy. You're not Superman.

Clark: I know, but even if I was--

Lois: Superman would find a way to save us. I know he would. I know he will.

Lois: You know, I have a funny feeling that you didn't tell me your biggest secret.

Clark: Well, just to put your little mind at ease, Lois, you're right.
Ides of Metropolis