Uh oh: It looks like Barry is using the Speed Force to mess with history again, or at least that would be the case if Superman & Lois hadn’t quietly severed its ties to the larger Arrowverse, because Clark and Lois’ son Jonathan is going to look a little different when the show comes back for its third season. We don’t know if there will be an in-universe explanation for it (is there a Superboy Prime in Superman & Lois and has he ever punched the walls of reality?), but there is a real-world explanation for it.
According to Deadline, Jonathan Kent actor Jordan Elsass will not be returning to the show for season three “due to personal reasons,” and so his character is going to be recast. Apparently, Elsass “did not report back to work by the deadline given to the cast to reconvene in Vancouver” because of a “personal matter,” but there are no details beyond that at this point. In a twist to most versions of the Superman canon, Superman & Lois features its eponymous couple having two teenage sons, Jonathan and Jordan, effectively making them as important to the show as the two title characters.
Recasting Jonathan, then, is a pretty big deal. Recasting in the Arrowverse isn’t totally unheard of, with the inimitable Caity Lotz replacing Jacqueline MacInnes Wood as Sara Lance in Arrow when the writers decided to bring the character back after her apparent death and beef up her storyline. That worked phenomenally well, as did Javicia Leslie’s well-received run as the new Batwoman on Batwoman (though the show was canceled not long after due to The CW’s still-ongoing money woes). Unfortunately for Superman & Lois, it’s technically not part of the Arrowverse, it just happens to feature the same actors for Superman and Lois (and also Arrow character John Diggle showed up once), so there’s no way to tell how this might work out.