MLB question: Substitution and video review

In yesterday’s Cleveland-Detroit game, Jose Ramierz was “hit by a pitch” and sent to first base. Cleveland took him out of the game as a precautionary move and sent in Gonzalez to pinch-run.

Then Detroit asked for a video review, and it was shown that the pitched ball hit Ramirez’s bat as he dropped it before it struck his arm so it was ruled a foul ball rather than a hit batsman.

So my question is, has the substitution of Gonzalez already taken effect. Could Cleveland have said, in that case, we want someone else to finish the at bat and the Gonzalez substitution never took effect so he could be put in defensively later?

It seems like that is the “fair” interpretation, but I’m not sure it’s covered by the rules. The only thing similar I know is when a game is replayed after a successful protest, any substitution after the protest is deemed not to have happened when the reply commences from the point of a protest.

From Major League Baseball Replay Review Regulations

Section II, subsection I

Effect of Replay Review Result on Post-Play Decision by Manager. If a call is overturned on Replay Review, any decision made by a Manager after the play and influenced by the incorrect call shall be nullified. Such Manager shall be permitted to reaffirm or change his strategic decision based on the result of the play as determined by the Replay Official.

Thanks, I looked all through the Official Baseball Rules. I didn’t realize these were separate.