Researchers and commentators have suggested several possibilities, none of which can be confirmed from the current evidence:

Migration and replacement: A population from outside the plateau — in this case, eventually identified as having Central American-related ancestry — moved into the region and became demographically dominant, either displacing the earlier inhabitants through competition or absorbing them through intermarriage in proportions that diluted the Checua genetic signal below detectable levels.

Population decline followed by replacement: The Checua-related population may have experienced a significant demographic decline — due to disease, climate stress, resource depletion, or other factors — that left the plateau partially depopulated, creating conditions in which incoming populations could establish themselves without resistance.

Disease: Epidemic disease has been a powerful mechanism of population replacement in the Americas.