I found very little about that.

I heard thing about now gone "repurposed churches" in mesoamerica, but I don't know what to think of that. (can anyone tell me more about this, I really would like to know how and if christians prayed in one of those mayan temples, because that sounds really awesome)

Though you may be interested in how the few Christians in Japan mixed Christianity and traditional buddhist ancestor worship after Japan became isolationist. History_of_Roman_Catholicism_in_Japan

But you can't really call that the offical church having a part in that. I think it can be said that there just wasn't a tolerating, multicultural mindset back then compared to now.