The answer is still incredibly simple, when it goes to replay, the replay officials simply review the play and make the call as to what they see, completely ignoring what the umpires call was.
If its definitive, they make the call. If its inconclusive, the call goes to the offense.
Ignoring the call on the field eliminates this issue. It will never happen, but that's the solution. And secondly, have a the umpire make a quick clarification announcement like the refs in football or hockey do.