The Chickens are in the Hayloft.

I think he did get used to being with her, but given how he quit flirting with other females and, at the end, was wondering about marriage and kids (shown in the episode following the one where Jeanne left), I think he didn't realize he'd fallen in love with her until he had already fell. I think he's tried to convince himself that it was all part of the op, but I think there's more to it than even he knows.