Score the run?

[Mrumpiresir]

An analogy. With two outs, if a runner misses the first base to which he is forced and is subsequently called out on appeal, no runs can score. For example, two outs, runners on first and third. Base hit to the outfield but the runner from first misses second and is called out on appeal. No run scores.

Of course there is no force at first but if the batter-runner misses first, the same principle applies.