If the batter runner missed first and was put on on an appeal, no runs would score. The game is still tied 5-5. If he missed any other base and was put on on appeal, the timing play comes into effect. Since it's no longer a walkoff home run, I'd say only one run scores and the final score is 6-5.
(This is somewhat similar to what happened in the famous Harvey Haddix near no-hitter in 1959 when Hank Aaron had a brain cramp and abandoned the basepath.)
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