The Americas in general, and the Amazonian Terra Prieta complexes in particular, do not need a lot of crops added to their inventory. Any crops from the Old World to the New are going to be a help, to be sure, but the fact is New World agriculture contributed far more crops to the global system than the Old World did. It was something Native Americans excelled at, developing far more crops than caught on in the Old World, so much so that reasonably good crops developed locally often were abandoned when better ones from elsewhere in the Americas reached various regions.
What is needed for Amazonian civilizations to survive is much better disease resistance. The OTL complexes did not vanish because their crop complexes were inadequate, but because plagues wiped them out so that the scattered survivors were too few to sustain their agricultural systems. (Indeed it is said that a great many "wild" species of Amazonia and elsewhere in the Americas, such as the nut trees of North America, are in fact cultivars--had there been no humans in the Western Hemisphere the wild plant inventory would be different, and in fact the incidence of useful plants in North America had to do with large area cultivation practices, like setting annual fires. To an extent the Native American inventory of cultivars included "crops" that required very little labor to sustain and are in a half-assed way sustainable with no cultivation at all; one can survive in Amazonia knowing the good plants that are now feral--because they had been cultivated to be useful earlier!)
Thus, the question is better posed in terms of what process might have given the Amazonian natives enough disease resistance to sustain their societies after exposure to Eurasian diseases.
If a light trickle of contact between Old World peoples and Amazonia had gotten started very early, but kept to a low intensity, I suppose very sporadically something nasty would make it across the Atlantic, and nearly but not quite devastate the Amazonians. After many waves of such exposure, we might suppose they are better prepared to survive the intense dumping of every horrible pathogens the Spanish and other explorers and exploiters would be bringing in the Early Modern period.
Perhaps. The New World peoples, unfortunately, had gone through a tight genetic bottleneck that severely limited the repertoire of immunity related chromosomes.
If in addition to bringing the "gift" of an occasional plague, the Old World visitors also were to intermarry with the locals, then Old World genes would spread, and of course these would be strongly favored during the bouts of plagues.
It is also the case that culture has something to do with survival of plagues; since epidemic disease was unknown in the Americas before the European invasions, Native societies were ill-equipped to deal with them; the mass despondency left them all the more vulnerable to military conquest.
If early trans-Atlantic contacts had caused the occasional outbreak in Amazonia, I suppose these plagues would radiate outward to all South America and onward to Central America and the north. Actually diseases don't spread easily among gatherer hunter peoples in sporadic contact, so they would only spread along lines of developed trading contact, which would tend to burn out those lines of communication and leave peoples more isolated than OTL on the whole, so there is a certain amount of natural self-checking.
Still, a major feature of Andean civilization was in fact interregional trade--over very short distances, because it was altitude rather than latitude creating the climate differences that drove trade. Trade up and down the mountains allowed each region access to more diversity of foodstuffs and other useful items than could be grown in their immediate neighborhood. So I do think that diseases propagating up the Amazon system would reach Andean trade networks, which did to an extent reach into Amazonia though they were centered more on the western slopes and altiplano. So at any rate South America would be strongly affected, and assuming the Andean peoples recover enough to sustain their development (probably somewhat delayed and stunted, but they reach back very far in time) they in turn would become a disease reservoir exposing Central American civilizations, and eventually infecting trade networks up the Mississippi as well as, I suppose, reaching the Pueblo peoples. And although gatherer-hunters in general tend not to be exposed until some traders from more intensely developed civilizations reach a particular band, California had an unusually high population density and when the Spanish decided to send the missions up the coast, decimating plague hit them too--so I suppose here some Mexic traders of some kind will spread it there too, eventually.
It is possible that the diseases will co-evolve with their highly vulnerable populations, favoring milder forms that don't kill them off as much, thus doing the work of broadly "inoculating" the societies--mainly by cultural preparation because there are few strong immunity chromosomes to select for in the population.
There is another feature of the immune system that is relevant too, which is that a developing infant and child's system can be "switched" over to either deal more effectively with macro parasites--worms and so forth, that are the main threat to scattered gatherer hunters mainly threatened by generic parasites not adapted to prey on humans particularly, especially threatening in warm humid climates favoring worms and so forth and making human direct contact via bare feet or wading or swimming in water more likely. Or alternatively with micro parasites which are the common threat in colder and drier climes where human civilization makes for denser human communities favoring the evolution of microorganisms that prey on our species. The Americas had civilizations, but they lacked many domestic animals which are the typical source of many terrible pathogens.
Thus Old World diseases filtering into the New World via the Amazonian peoples might indeed coevolve to be milder, but still do the good work of preparing the Native civilizations generally by both cultural learning and by switching their immune systems over to be more prepared for micro-infection. If that does happen then I suppose they will suffer more from macro parasites like worms though.
The vast majority of Native New world peoples will still lack much genetic diversity and will still suffer much when exposed heavily to the whole package of Old World diseases in huge doses such as the Early Modern invaders will bring with them. But perhaps all across the Americas, and especially in South America, they will survive better, falling less far and being less socially disorganized by plagues when they come, and thus prove more difficult for Europeans to subjugate or replace wholesale.
Getting back to Amazonia--if a trickle of ongoing light contact is sustained for many thousands of years, and the Old World visitors do interbreed with the downriver natives, a spectrum of peoples particularly resistant and resilient will exist there, as the survivors of successive plagues will have higher concentrations of Old World genes that will spread in a Darwinian fashion. I don't see this process as spreading them all over South America, indeed not very far up river unless Old World people find reasons to personally travel up the rivers a lot, which I don't suppose will happen. But maybe instead of being so vulnerable that a handful of Spanish explorers spread diseases so awful that the entire set of societies all collapsed promptly, so much so that later generations of European scholars simply assumed the conquistadors were making up stories out of whole cloth, the Amazonians in particular will be far less vulnerable than usual, and prove to be very tough nuts to crack indeed, being capable of retreating up the rivers into jungle environments that baffle the Europeans and hold hidden threats--threats so nasty in the hands of knowledgable natives that they have to give up and rely on voluntary contact at downriver trading posts, leaving the river peoples more or less free to adopt and adapt European stuff as they see fit. Possibly as in other places the Spanish found main force to be useless, missionaries will infiltrate and draw the native peoples in on a more voluntary basis.
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But in fact if there is sustained light contact across the Atlantic for any period of time well before the 1500s CE, then that will probably greatly butterfly developments on both sides of the Atlantic.
I gave a Like to the suggestion that West Africa will be brought into steady contact, for instance. Even if we take the Sahara as a cultural butterfly net preventing any substantial changes in European history, which may be quite a dubious thing to assume, with American contact and ongoing trade, West Africa will presumably develop somewhat differently.
And if a consequence of this is expansion of contact and trade of Amazonian river mouth peoples across the Atlantic, and up and down the Atlantic coast (will the Orinoco river system be colonized, from mouth upstream, for instance?) then eventually they can reach the Congo river mouth, and I'd think that Amazonian cultivars would then make their way fast into the heart of Africa, and enable an even higher level of development there than the already remarkable levels the Portuguese found OTL. To West Africa, add the Congo region as vastly more populated and developed than OTL.
In fact any cultural butterfly nets the Sahara lays down will be weak and full of holes; news of a wealthier West Africa and Congo, probably carrying with it some tales of yet more rich lands beyond the great ocean, will attract attention from East Africa and possibly the Mediterranean world much earlier and stronger. The fact is it is easy enough to get to West Africa from the mouth of the Mediterranean--but not so easy to get back to the straits against prevailing coastwise winds and currents! If however our Mediterranean adventurers meet locals who know how to get to America and back again, using these gyres it is much more feasible to get back to Europe if they can learn how.
If for some reason the Mediterranean world ignores all this (not necessarily inconsistent with Phoenicians starting it all--they could keep secrets pretty effectively) then long before 1500, the Islamic world (assuming it is not butterflied, but even if Islam is, presumably the peoples making up the Islamic sphere will remain active on different terms in the ATL) will seek out routes across the desert or south of it to West Africa, and thus the news of places as far away as Amazonia itself will be brought to the Old World's most ancient centers of civilization. If Amazonia is not on European maps, it will find its way onto Arabic ones.
Thus even if we have Europe proceeding in total ignorance of all this, when we eventually have the Iberian explorers expanding, they may well find that not only West Africa but the Congo and Amazon are all Muslim, at least to a light degree. And the Spanish, that the peoples of the Caribbean do not die off so easily, and when forcibly gathered to serve as forced labor, can organize themselves into effective rebellion. The Americas in general will be less places that Europeans can shove aside the native peoples and set up their own little colonial paradises in, and more places like Africa or Asia where they must form some kind of political relations with the people already there.
And perhaps European expansion is checked to a great degree by a Sultanate of the South Atlantic.