Indeed the obvious building material would be wood or even just other vegetable matter, thatch and vines for lines, etc. They would have to do earthworks and indeed in Charles Mann's
1491 IIRC there is extensive discussion of just such remnants being observed via satellite, and informed by that, aerial surveying, since followed up by observations on the ground, which link up to Conquistador accounts of numerous very large settlements on the rivers they explored. All sorts of evidence shows that there was a tremendous population implosion presumably due to these same explorer/conquerors spreading disease in the usual fashion. So--one would search for a tiled stone city in vain, perhaps, but why should an advanced agricultural civilization complex be obliged to prove its existence by stone works, when the sensible thing for them to build in is abundant wood and other plant and perhaps animal materials? It means when they fall and their structures rot away we can't find traces hundreds of years later, but while they thrived, why build in stone? A particular settlement might find stone handy perhaps, but they generally would not in the river bottom jungles.
I've seen the basilica in St Louis that was the Spanish capital of the whole vast Louisiana Territory, then the cathedral of the Spanish theocracy over the region, and it is made of wood too. Presumably if humanity were struck dead and it decayed naturally it would leave a few more traces than possible ancient Amazonian wooden cities might, between rusting nails and shards of stained glass windows, but plump that sucker down in the middle of Amazonia and forbid anyone to maintain it and how fast would the termites eat the bulk of it? How long before it is swamp mulch, washed down the mighty Amazon to the sea? Would the mighty conquistadors, should they have by some miracle of God avoided destroying their prospective subjects en masse, having subjugated some hypothetical large fraction of the ppulation, large enough to support their imperial structures and auxiliary gold and silver hunting expeditions on the lost Terra Preta methods of jungle cultivation, have built their cathedrals and presidios in anything but lumber themselves, so far up the rivers in the midst of the soggy jungle? I suppose they would indeed eventually resolve to build something in stone, but they only could because of being an order of magnitude more advanced technically and ruling an empire of truly global sweep, expensively importing marble and granite from thousands of miles away, and probably finding that heavy stone structures sink, well, like a stone, in the swampy earth. Maybe a really visionary architect could foresee the problem and make a raft-like foundation it can float on, perhaps.
Stone would be extravagant and seem unnaturally foolish to the Amazonian peoples I would think.
If they in fact did have slow contact with West Africa, they might or might not take up metal working. I don't know what sorts of deposits are to be found in the region. Partnering via trade with the Andean peoples would be quite likely, and apparently did happen. (The major driving force of complex civilization in the Andes was the great range of climatic biomes to be found over a short horizontal distance since these were often substantial vertical distances, so trade between different types of cultivation at different altitudes enriched people at all points. This mainly developed on the Pacific slope but trading east into Amazonia would be quite a natural extension for the highland peoples).
The trick is to get so much contact with Africans that a significant share of the population deep in the region, far up the rivers, shares African genes, but not so much that Amazonia is well known to the ancient Old World. Or what the heck, why shouldn't it be? The barrier is that crossing the Atlantic is inherently difficult, a matter of ancient sailors lacking good food and water storage reliable for such long trips out of sight of land, plus of course navigational issues and questions as to whether people before 1500 CE or so could build ships that could hold together reliably for the long crossing. West Africa to eastern Brazil is the short path of course, and conceivably West African coastal peoples might get wise to the current and wind gyres. Or conceivably, American natives might do it. The trouble with that is that the Amazonian river peoples don't seem to have ventured out onto the oceans, but perhaps we could have a scenario where Atlantic coastal peoples near the river mouth are motivated to try. The better bet is West Africans figuring it out I think, they have better access to the evolving Old World technical lore. But to get the Amazonians intermarried with enough Africans to give them a firmer resistance to the Eurasian plagues suggests to me an extremely long period of contact, thousands of years, and even so probably requires really large migrations of Africans westward, which throws into doubt whether Terra Preta would develop at all. But OTOH Mann and others suggest that much of the foundations of New World civilizations were quite ancient themselves; there is evidence of major human transformation of landscape ecology going back a great many thousands of years, so African influences would seem more likely to supplement rather than preempt the New World developments.