By removing Lavos, you mean that it would just spontaneously disappear from the time line after dragging Chronopolis to the past, right?
Anyway, theories or not, I'd imagine that at the very least, since the Time Crash is the turning point, obviously anything before it would be retained. Dinopolis may or may not be dragged over depending if it was done due to Lavos itself, or Chronopolis itself. Then either events go as "normal" until 1006 AD, or they do so with a Dragonian-less El Nido.
Before going any further, I have a question of my own. What would this mean for the DBT? Would a version of Lavos still be there to merge with Schala?