The Aquiry civilization (that this paper is about) actually ceased (either due to collapse or people changing their mind about that way of life, who knows) between 850 and 1000 CE.

And WDYM "anyone"? Obviously plenty of people met them and plenty of civilizations derived from them. By the time Europeans got there, the Amazon Basin was home to 5-10 million people (some models push it up to 20 million). I'm sure traces of that culture and history still mark those indigenous cultures today

Not all - it is very likely this large Amazonian civilization perished before the Iberian colonists arrived in the region. For example, these geoglyphs mapped in the (super interesting!) paper are dated 2k years before the Europeans first arrived in Brazil.

The really haunting part is that Europeans often arrived late enough to see the collapse, but not early enough to understand what had collapsed

It really is a strange and horrific metaphor, analogy, and parable about the effects of isolation - made all the more distressing because it wasn't intentional. It was just our broader ancestors going about their business as normal people.

The same thing happened to the native North Americans too. When the Pilgrims showed up in Massachusetts in 1620, the whole region between there and maine had been reduced in population by 90+% due to a plague inadvertently brought by traders

Spain and Portugal were under Umayyad colonization when this civilization died.