Trying to come up with a good example here. Let's say runners first and second. Batter hits a liner to the outfield. The fielder makes a play, the umpire rules it an out, the runners scuttle back to their bases. But the play is challenged, replay shows the ball bounced on the field first. What happens? The runners at this point are in jeopardy. You can't just award them the next base, that's not in the rules. You can't give the ball to the right fielder, restart the play and give him a shot at an out on the bases.
Seriously, what happens in that situation?
If the baserunners reached base safely, I'd say re-award them the bases. Simple.