The Time Crash is very anomalistic, as it exposed the entire Sea of Eden to Lavos's will and resultingly traveled back in time ten thousand years. What are the exact mechanics surrounding this event? GrayLensman extensively addressed this question for the Salt for the Dead Sea article. Taken from there, here is the theory concerning the Time Crash.
The Time Crash was completely unlike standard forms of time travel.
- Chronopolis and Dinopolis contained many more than three entities, violating the Conservation of Time theorem.
- A three-dimensional region of space, containing a vast area of the earth's surface, was transported. This is opposed to Gate travel, where the horizon of the Gate acts as a portal from one space-time to another. Gates displace their spherical volume in normal space-time -- they do not envelop a region of space and transport it through time.
- The area of the Sea of Eden was still linked to the cause and effect of the future. Unlike normal time traveling, where travelers are not affected by changes to their past world line, the Sea of Eden changes along with the timeline. In Home World, the Day of Lavos still occurred and Chronopolis changed into the Dead Sea, reflecting the ruin of the future.
The conclusion is that the region of the Sea of Eden containing Chronopolis in the Chrono T-2 dimension and Dinopolis in the Reptite dimension did not time travel at all. Rather, the counter-time experiment created a space-time warp which brought the space-time coordinates of the area surrounding the Sea of Eden in 2400 AD into conjunction with the space-time coordinates of the Sea of Eden in 12000 BC. The substance of Chronopolis and Dinopolis was not transported through time; a region of space-time in 12000 BC became that same region in 2400 AD.
The edge of the Sea of Eden was separated from the space-time of 2400 AD and connected to the space-time of 12000 BC. The Sea of Eden and the rest of the world both moved forward through time at the normal rate so that in 1020 AD, Chronopolis was in 15420 AD. The boundary of the Sea of Eden anomaly allowed an entity to travel 14400 years into the future. Passing through this boundary is exactly like time traveling through a Gate or in a vehicle. Time is Conserved and travelers become immune to timeline changes.
In 2400 AD, I image that the Time Crash would appear as if the area of the Sea of Eden collapsed into a singularity. A hole was made in space-time, and the edges of the hole were pulled in to fill the void. In 12000 BC, the future Sea of Eden space would expand from a singularity, enveloping the past Sea of Eden.
When the timeline was changed so that the Time Crash did not occur, the Sea of Eden in 12000 BC remained unchanged. The version of the Sea of Eden which contained Chronopolis was sent into the DBT. However, the boundary of the Sea of Eden behaved like a Gate, even though the space-time anomaly no longer existed. Any entities which crossed the boundary from the future Sea of Eden into the 12000 BC world were protected from changes made to the timeline. Each time an entity crossed the boundary from the Sea of Eden in the original timeline, that same entity appeared at the boundary in the new timeline. The settlers of El Nido appeared out of thin air at the edge of the Sea of Eden. If and when the entities returned to the Sea of Eden in the original timeline, the new versions of the entities were sent into the DBT, in accordance with the Time Bastard theory. Since the outside world was identical in both timelines, the new versions of the entities ceased to exist just as they crossed the conceptual boundary of the Sea of Eden, maintaining the illusion that anomaly was still there. Thus, El Nido was constructed and settled by humans and Reptites, even though Chronopolis and Dinopolis no longer existed in the past.
An unfortunate consequence of this theory is that any entity to ever exit the anomaly must appear at the boundary of the Sea of Eden regardless of changes to the timeline. It is not known how many entities exited Chronopolis/Sea of Eden/Dead Sea after 12000 BC (in Another World only, of course), but they would end up wandering around the new timeline. Some of these entities would eventually be sent into the DBT as a result of the Time Bastard theory if they originally time/dimensional traveled. Maybe Schala could have just sent them all into the DBT. This problem could be potentially far-reaching.
The ramifications of this theory are fully addressed in the Chrono Cross Resolutions article, which explains the aftermath of Chrono Cross's unification of dimensions.