The Harrapan or Indus Valley Civilisation vanished in a period of around a 100 years c. 1800-1700BC. Best bet is that climate change shifted the monsoon, deforestation caused by excessive use of kiln-fired bricks and economic changes disrupting trade with the Middle east caused a collapse and the population migrated south to form a village culture rather than a city based one.
Classical Mayan culture disappeared over an 80 year period. The inhabitants just walked off into the jungle. Also put down to a prolonged drought.
The Minoans. Rulers of the Mediterranean, most advanced culture of their time--gone in a flash--possibly the Thera volcanic event and tsunamis, maybe the sea-people's invasion, perhaps a combination.
The Olmecs. the Olmecs didn't "turn into" the Toltecs or the Aztecs. They disappeared. Perhaps earthquakes, perhaps volcanic eruptions, perhaps climate changes caused by El Nino events. But they went.
The Great Zimbabwe. Still a mystery. How did the incredibly primitive Shona precursors build such a sophisticated society and then suddenly turn back into an incredibly primitive society again? Perhaps the founders really were the Phoenicians, the Jews or the Arabs. The Queen of Sheba and King Solomon's Mines ring true. Aliens maybe?
The Cahokians of Illinois. Mound builders, a city with a population of 40,000 plus in 1250Ad just a short drive from St Louis? Vanished like a puff of smoke, just before Europeans arrived.