The Great Upheaval was a period in Skytopian history after the Great War, when pieces of the land were elevated into the sky. The upheaval was caused by the use of unobtainium weapons, most likely by the Defiers who fought the Children of Magnus in the war. The anti-gravity properties of unobtainium caused several chunks of land to break away from the ground and rise suddenly, while others fell and burned. Massive floods caused by the sudden cracking of the ground washed away most of the civilization on the world's surface, and only those who clung to the rising rocks survived.
Those pieces of floating land which were settled by the survivors are today's skylands. There may be many more skylands which have not yet been discovered, although without the use of skystone to balance them they may have already fallen from the sky.