Let's see... Spain can still conquer Haiti and Cuba, but instead of dying off, the locals can survive, flee into the interior, and resist forever. Spain has to put forth a lot more effort to hold them. If Cortes (or some other Spaniard, he barely got out of Cuba) invades Mexico, he might be successful, as all it takes is for the other Mexican countries to realize that resistance against the Aztecs is possible. But with the Mexicans remaining numerous and armed (no doubt adopting European technology as fast as they can acquire it), Spain will not be able to impose latifundias (is that the word)? Spanish governors in Mexico will eventually have to employ careful balancing act politics, meaning the Mexican nations retain a lot of independence. As for Peru-no way. Pizarro and his gang disappear, along with many another expedition.
And I'm sorry, but this really should go in ASB.