Mesoamerican and Incan civilizations were undergoing mass conversion at the hands of the Spanish at the same time European Christianity was being torn apart by the Protestant Reformation. Do we have any idea how these peoples conceived of the religious conflicts afflicting Europe?

I answered a similar question here. In short, the Reformation did impact the language of Catholic texts used in colonial Peru. Unfortunately, we have a very limited number of texts from indigenous perspectives from that time period. It's likely they would have been aware of such events, and my answer explains why it would have been in their best interest to not bring it up at all.