I was thinking with the modern outrage of Zika, and a vague remembrance of discoveries of piles of "disabled" corpses, mainly children, that maybe there was a connection?
They didn't? The Spanish waged wars of conquest against numerous Mesoamerican groups like the Aztecs, the Maya, the Caxcanes, the Zacatecos, the Chichimecas, etc. In fact, the last Maya kingdom to be conquered, the Itza, fell in 1697. And the Cora people were not conquered until 1721 after a combination of drought and disease weakened them enough for the Spanish to attack them in their mountain settlements. Besides these wars of conquest there are millions of indigenous people alive today in Mexico, Belize, Guatemala, El Salvador, and Honduras.
Perhaps you are thinking of the Classic period Maya Lowland abandonment? If so, I would suggest checking our FAQ which has several well answered questions on the event.