Certainly not all of them, but in certain areas it's quite possible that refugees have been mixing with local population, or even forming new tribes. New resear

Certainly not all of them, but in certain areas it's quite possible that refugees have been mixing with local population, or even forming new tribes. New research data all indicates that there were some, for that time, huge cities (100+K population) in Amazon basin. It makes sense to presume that when epidemics started at least part of the population managed to escape into surrounding jungle, leaving those cities empty, similar how in Europe many cities have been completely deserted in the time of plague. Obviously, we know so little about this that it's all just a speculation.