Here's what happened...
The umpire at 1B immediately called a balk on Meyer for not coming to a set position for a one-count. However, that is not a balk when you throw to any base besides home. Meyer's move was apparently so good that it fooled the runner AND the umpire at first into thinking he was going to the plate, hence the balk call.
Now, a balk is technically a "delayed dead ball." Once a balk is called the runner is no longer in jeopardy, and this is why the runner was not out at 2nd base. MJ came out to argue that the pitch was not a balk, which it wasn't, and the umpire reversed the balk call.
(Here's where Scalise, a former Cougar High player himself, tossed an F Bomb before earning an early trip to the shower).
So, the runner cannot be in jeopardy since the delayed dead ball (balk in thise case) was called, so the runner is not out at 2B. Therefore, the runner was assigned back to the last base he had earned before the delayed dead ball call, which was first base.
In effect, a "do-over."