We know that European settlers did a fairly thorough job of destroying the native culture of the Americas. Megaliths of the Northeast were dismantled to provide stone for their own buildings. There was nothing in the way of archeological protections 400 years ago... the 'heathen' sites had no advocates for preservation.
Mystery Hill in New Hampshire is one of the sites that wasn't entirely hauled off for stone... I still need to go check it out sometime.