I think the general idea we chose to reconcile the entire Project Kid stuff was that the entire Sea of Eden is one big TTI zone. Going into the Sea of Eden is effectively traveling thousands of years into the future. This would mean Project Kid/Chronopolis/Sea of Eden's existence is always assured, and Belthasar of the future no longer has to initiate anything to make it happen again. Everything's protected by TTI.
On an even simpler level, the act of Serge and his party going into the Darkness Beyond Time is considered a TTI-granting event, as if it's a form of time travel (just as visiting the End of Time was for Crono). A version of Serge is always going to pop out in the Darkness Beyond Time's own time axis at some point, even if the world he came from never existed or were destroyed. And that version of Serge is also eventually going to be TBd and a new version of Serge will pop out in 1020 A.D., having just defeated the Devourer. No need to repeat anything.
