What immediately came to mind (and may or may not work for you) was a paradigm shift. It comes from the work of Thomas Kuhn in the book The Structure of Scientific Revolutions (1962).
*Note: I will probably not do his argument justice in a few lines.
The basic idea is that scientific theories encounter anomalies that cannot be explained by the rules that are part of the scientific system. For instance, Newtonian physics was thought to be the be-all-end-all scientific paradigm for years until Einstein challenged Newtonian physics with his theory of special relativity. The dominant theory is thrown into chaos, attacked from all sides, its weaknesses exploited, until another stronger paradigm emerges.
Another example, related to your own example about how people changed their view of the universe, is the shift from a geocentric model of the universe to a heliocentric model. For years people believed that the Earth was at the center of the universe. It wasn't until the works of Copernicus, Galileo, and Kepler emerged to challenge this model that the gradual change to a new paradigm (the heliocentric model of the universe) began.
This seems to be a description for what you are looking for -- a gradual refinement of knowledge over time.