Ok my interpretation of the MLB rule book
section 5.08
shall disallow the run, call out the offending player and order the game resumed. If, with two out, the batter-run- ner refuses to advance to and touch first base, the umpire shall disallow the run, call out the offending player, and order the game resumed. If, before two are out, the batter-runner refuses to advance to and touch first base, the run shall count, but the offending player shall be called out
7.10 Appeal
states that an appeal must be made by the next pitch or before the team Abandons the field.
my read:
in this case umpire could call him out. If he fails to call him out the team in the field could apeal. Absent the appeal he is not out and gets credited with hit. Same as if he missed first base