In reading your sitch..... if the defense didn't see it, and the umpires didn't see it, how did anyone know the 'play' was run?
You gotta be kidding....another "solution" in search of a problem. 'Oh gee, it just doesn't
seem fair, how can we invent a rule to 'fix' this?'
There's a specific section of the rulebook that addresses this very issue: it's called, "Appeals."
If it occurs and NO ONE appeals, then it is legitimized - end of story. If there's an appeal, rule on it. If the umpires did not see the missed bag, then they erred, simple as that. You cannot call what you did not see.
Why penalize the offense for the umpires' mistake, and subsequently the defense's mistake in not seeing the missed base?