Much of it was deliberately destroyed and obscured. Large parts of Cahokia were destroyed by highway and suburban development, and it wasn't that city planners and officials didn't know it was there. They often suppressed discoveries and tried to cut archaeologists out of the loop, because the artifacts and etc were in the way of development goals.

Many North American cities were built on top of or near where native settlements were. It was in the best interests of colonials and moderns to suppress or diminish findings.

That and North Americans were engaged in a long running cultural genocide based on a mission of Christianizing a 'primitive' people, which would have been undermined by recognizing this area as previously occupied by a settled agricultural societies.

https://www.amazon.ca/Cahokia-Ancient-Americas-Great-Mississ... is a great book on this topic written by an archaeologist who spent much of his life working around Cahokia. And he gets into this issue at length.

I read this book some years ago: https://www.amazon.ca/dp/B002FQOHTW

It was really good. But to your point, I'd say: don't assume that Europeans didn't believe the Plains Indians were incapable of the monumental architecture so much as a good many of the settlers actively wanted that knowledge suppressed, primarily for their own economic reasons (if it was on your farm land you made a living on, what would you do?)

A good portion of the potential sites were deliberately destroyed. Especially in the modern era. Huge battles about strip malls, highways, parking lots and other construction. People knew to some degree what was there and the fact that it was there was inconvenient to the other narrative: the rise of America and its glory. So artifacts were destroyed and sites suppressed.