The sub assumes the count.
It's not specifically stated in the Rules Book, but 3.1 does state that, other than the starting pitcher, "in any other case, a substitute may replace a player of his team when the ball is dead and time has been called." The NFHS Case Book has the following situation:
3.1.1 Situation: B1 has a count of 1-2 when the captain or coach decides to put in pinch hitter S1.
Ruling: The coach should ask the umpire to call time to make a substitution. When S1 enters, he is charged with one ball and two strikes. If S1 strikes out, the strikeout and time at bat are charged against B1, since he he had more than half of the allotted strikes. In any other case, the time at bat is charges to S1.
Note that this is not necessarily a charged conference, but rather a time out to kill the ball so a legal substitute may be inserted. In the situation you stated, I would charge an offensive conference since the coach came out and conferred with the batter before making the substitution. If there had already been a charged offensive conference during the inning, I would not permit the coach to come out, but would allow the time out for a substitution to be made.