Frankly I'm surprised there aren't like 52 Superboy Prime's around.
See, he was pushed into the Speed Force. THe Speed FOrce exists outside of time. So even though Mr Mind altered each reality, there was still a period where they were identical to New Earth. Where a Superboy Prime was pushed into the Speed FOrce by Bart Allen, with the help of Barry, Max and Johnny Quick. So they should have to come out somewhere.