I think that, realistically, Elias doesn’t want kids. However breeding kink/pregnancy fixation demand that he knock up Jon, so consider:

Everything is going great, business as usual, his new archivist doesn’t yet know of the future that awaits them both but is making so much progress already, and then BOOM. The Eye helpfully informs Elias that he accidentally got Jon pregnant. Now the thought of children? Noisy? Demanding? In the way? Gross. Bad. No thank you. When he was still Jonah, still theoretically capable of conceiving, the idea disgusted and frightened him, and once he found a more… suitable vessel he didn’t really reevaluate that thought. But suddenly he’s forced to consider it again 200 years later and now its more fucking Complicated. First off, the concept of Jon pregnant? Appealing. A permanent mark of ownership. A part of Elias growing inside of Jon and fundamentally changing his body. Elias accidentally walks face-first into a brand-new pregnancy kink. Whoops. Secondly, a weird, mix of gender euphoria and pride. He fucked his archivist so good he got him pregnant. And like, sure. He was theoretically aware that he could now get other people pregnant, but it hadn’t really sunk in until this moment, and its bizarrely validating for his Gender.

Still massively inconvenient tho. And now he needs to either tell Jon or wait for him to start developing symptoms. And it’s a whole fucking mess. And a very self-indulgent part of him wants Jon to keep it just so he can see Jon swollen with his child, no matter how badly things get tangled from there.