No, because the actual 3rd out came on the "next play" during the "next batter". The HR play was over and done.
As a matter of course, if you have an automatic out, be sure not to call it too early (especially in cases like this one). Wait until action has stopped and it is obvious there is no further action from the defense (such as an appeal). I even take the extra step of separating the plays by walking over to the scorekeeper after I decide the play is over (even if he/she had been yelling, "That's 3, blue, automatic out is next!"), confirming the 3rd out, and then announcing it.
Once you announce the player out for not batting, anything that happened on the previous play is moot (BOO, missed base, etc). In effect, allow time for the missing batter to come to bat before calling that batter out.
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"Many baseball fans look upon an umpire as a sort of necessary evil to the luxury of baseball, like the odor that follows an automobile." - Hall of Fame Pitcher Christy Mathewson
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