See, I just don't see it that way, I guess...Sequels are greatly tied to originals, but many times, they act as separate stories
and in about 99.9843% of the time, they really are. Let me put this into perspective directly in relation into the Chrono series.
We have the ds gameplay conversion being revealed; spiffy keen. It can share the love with more people. However, once again, they're going to be adding to it, probably to help further justify the slop that is Cross, just like with the playstation release. Pending the success, and meaning, of what they choose to add, does that then change Trigger? Probably not. If its consequential at worst, reviewers will phase it as something like 'it was great, except for that... and so on" its extra, though probably going to be 'canon'. In effect, any bad out of this would, as you say, largely effect just the reputation of the series, and further works, rather than the original.
But, its still the sequel trying to make a change on the original, and one, imo, for the worse. The tip of this is to me, while Trigger had some loops and holes and what not that have great potential for a sequel of events, Cross has snipped that. (but not completed cut.) That lack of 'cannon' potential does effect the story. If the potential means didn't have a weight to the quality of the story, then no one could be success from 'trying to leave things up to the audience.'
So:
Wouldn't Schala know?
I'd rather Schala have not been in that particularly written predicament anyway, as I find the 'how's and 'why's and the 'whatnots' that got her in and out poorly conceived. She'd be better off not knowing because it 'didn't happen.'