"9.02(c) If the umpires consult after a play and change a call that had been
made, then they have the authority to take all steps that they may deem necessary, in
their discretion, to eliminate the results and consequences of the earlier call that they
are reversing, including placing runners where they think those runners would have
been after the play, had the ultimate call been made as the initial call, disregarding
interference or obstruction that may have occurred on the play; failures of runners to
tag up based upon the initial call on the field; runners passing other runners or missing
bases; etc., all in the discretion of the umpires."

http://mlb.mlb.com/mlb/downloads/y2014/official_baseball_rules.pdf