Necromancy on an eight year old thread.
I've had a theory on the basis of the Counter-Time Experiment conducted by Chronopolis, Annihilation Energy, and the very nature of time travel in Chrono Trigger. It is not based on actual science and there's probably room to poke holes in my theory, but it is based on what we know of confirmed Chronoverse time travel mechanics.
Based on what we've seen in Chrono Trigger, time travel mostly works like it does in Back to the Future. There's a singular timeline that, when there are changes to the timeline, the previous timeline gets "erased" and shunted to the Darkness Beyond Time, while it is replaced by the new timeline in which the change was made.
This contrasts somewhat with multiverse theory, something the Chrono series never really explores as a possibility but tiptoes upon this with the existence of the Reptite Dimension, the origin of the Dragonians in a timeline in which Lavos never descended upon the planet.
Regardless, my theory stems from the naming conventions of the project itself and currently doesn't have in-game dialogue to back it up.
Based on what we know:
-When a change to history is made, the original timeline is discarded to the Darkness Beyond Time, while the new timeline becomes the prime history
-Discarded timelines converge in the metaphysical, yet singular realm of the Darkness Beyond Time
The Counter-Time Experiment, I then theorize, was to try and utilize counter-time, namely the ability to retrieve and revisit discarded timelines. We've seen several timelines in the Chrono series - the original timeline in which Lavos destroys the planet, and a new timeline (Keystone Timeline) in which Crono and company stop him, which in turn results in Chrono Cross.
We know that Balthasar arrived in the new, non-apocalyptic 2300AD and utilized Central Regime resources to found the Time Travel Institute, Chronopolis, and Project Kid. His penultimate goal was to save Schala by any means necessary, even if that included creating an insanely convoluted plan regarding the near-murder of a child in order to move the Time Devourer/Schala just enough for Schala to regain enough humanity to create a sort of semi-clone. The Counter-Time Experiment was part of that.
What if the Counter-Time Experiment was originally intended to reach into these previous, discarded timelines and simply pluck Schala into the prime timeline. No need for a multiverse, and no need for the entirety of Project kid -- just reach into previous histories and grab Schala before she became part of the Dream Devourer entity. Problem solved.
However, the experiment failed and Chronopolis was hurled into the age of Antiquity, and we all know what happened from there.