He shouldn't have abruptly left on a long voyage at all and he really shouldn't have if he was so close/involved with her.
If we go strictly by what happened in S2, then he erased her memory of the whole thing, so they didn't have anything special going on at all anymore.
Either that, or he reversed time and the relationship never even happened in the first place, a la the rough/conjectural Donner Cut. But in the latter case, there's no way Lois could have been pregnant, so SR is nonsensical as an in-continuity sequel to the Donner Cut, despite Warner basically pushing the Donner Cut as the new "official" version of the movie by making the Lester cut unavailable as a standalone blu-ray in the North American market, and including the Donner Cut in a "Triple Feature" blu-ray set along with
Superman: The Movie and
Superman Returns, implying that the three movies are supposed to form a cohesive trilogy. And you also end up with Superman zooming around the Earth to reverse time two movies in a row, as this was originally intended to happen only in the second movie and not the first one.
To me, none of the Superman movies have been quite right, but Richard Donner's work comes closest.
Besides being rather underwhelming,
Superman Returns tried to heavily rely on nostalgia, while at the same time only fitting the actual narrative continuity of S1 and S2 in the vaguest and foggiest of disjointed broad strokes.
The DCEU (or whatever they're calling it these days) movies so far featuring Superman are ponderous, dour and joyless; a real chore to sit through. These movies' tone takes on a self-important air of trying to say something big and meaningful, but they really don't.
Kor