Hot damn, I am legit loving this thread necromancy!
I have recently been playing Another Eden: The Cat Beyond Time and Space, which was written by Kato. It's a time travel adventure that, as I was playing the main quest, I couldn't help but wonder if it hadn't somehow been the unused plot from Chrono Break.
The storyline is, essentially, that a scientist from a horrible future genetically modifies his children, with the intent that they all travel back in time and rewrite history using his genetically modified children so there is a new, better timeline. Things go awry when he is separated from them, and they grow up in a different era knowing nothing of their true origins. Eventually, the kids are pulled into events in which they are manipulated into changing the timeline, but it turns out that all of these changes are causing "time quakes" that threaten to rip space-time apart ("breaking space-time" a la Chrono Break). They end up having to undo their changes to the timeline in order to set things right, with the intent of finding another way to rewrite history... without destroying space-time. As of yet this hasn't happened, and the storyline is still being released in episodes.