R1 and R2 with one out. The batter rips a ball to the right center gap scoring R2 , however, R1 is thrown out at the plate. The batter pulls up at second base with a double. The defense successfully appeals that the batter/runner missed first base. R2’s run is taken off the board.
This is True because if the final out is recorded by retiring the batter/runner before reaching first base, no run shall score on such a play.