The first 5 seasons of The Flash had a newspaper detailing on how the Flash "vanished" in the crisis. As of Legacy, the Flash of Earth-1 while fighting the Reverse-Flash with a group of heroes. However, the Flash of Earth-90 vanished through destroying the Anti-Monitor's cannon.
Leonard tells the heroes that they have 28 seconds from the destruction of Earth-1 to the destruction of the Waverider, but the gap is actually about 45 seconds. However, it's possible that there was some time overlap during the transportation of the Paragons to the Vanishing Point.