From 9-1-1:
A run is not scored if the runner advances to home plate during action in
which the third out is made as follows:
a. by the batter-runner before he touches first base; or
b. by another runner being forced out; or
c. by a preceding runner who is declared out upon appeal because he failed to touch one of the bases or left a base too soon on a caught fly ball; or
d. when a third out is declared during a play in which an umpire observed a base-running infraction resulting in a force-out (this out takes precedence if enforcement of it would negate a score); or
e. when there is more than one out declared by the umpire which terminates the half inning, the defensive team may select the out which is to its advantage as in 2-20-2.
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The missed base does need to be appealed, but the result of the appeal is a force-out, because the runner was forced to the base that he missed. He didn't reach it safely.