You are viewing natural selection in action, or i guess it's artificial selection since you are the one choosing the trait. In this case flocculation properties. As I understand it a yeast flocculates based on proteins present on the surface of the cell. As time goes by, and cell reproduction occurs, there are random mutations, some of those mutations might cause a change in those surface proteins, and change the how effective the individual cells are at falling out of solution. So when you take the yeast that are left at the bottom of your secondary, you are harvesting the yeast that are the poorest flocculators, and throwing out all the ones that drop out of solution quickly. Do that a few times and you are left with a whole colony of yeast that are not as good at flocculating as the original strain.
The breweries that are using the same strain are growing them up from single colonies that they grow up through bigger and bigger starters, and like was said before, they are harvesting the yeast for the next batch from the ones that floc out like they expect from that strain.