Yeah you're not going to get around having a paradox when time travel's involved. I mean, no matter how good the stories are, they're still just games. Square didn't research physics to get things 100% accurate. It's too bad though =(

Either way, the game pretty much spells out that the timeline split when Serge lived/died. The whole basis for him destroying the future rests on the premise that two possible realities formed - one reflecting what would happen if he lived, another showing what would come to pass if he died.