Why then did the Creator seem to largely "start over" after large extinction events? Surely he didn't forget what he knew simply because an asteroid hit the Earth.

Now that you have put forward a theory, the proper thing to do is evaluate its usefulness. The most useful theories are easily falsifiable: it is easy to imagine scenarios in which they fail. For instance, if any of the planets followed a square orbit, Kepler's laws of planetary motion would be pretty much kaput. Under what situation would you consider it clear that our planet's species' evolution did not follow the mind of the Creator?