Shame on the runner for not going back to second when she was supposed to.
Shame on the third base base for not sending her back.
Shame on the defense for not bringing this up sooner.
But, mostly, shame on the umpire for not making sure the runner had returned before making the ball live again after the foul ball!
You're not going to find a specific rule that covers this- because it's not supposed to happen in the first place. This might be one of the very rare times that an umpire would have to apply rule 10-2-3g: "The plate umpire has the authority to make final decisions on points not covered by the rules."
Personally, here is how I would probably handle this (and I have never had to and hope that I never will!):
- If discovered before another pitch is thrown, return the runner to second without penalty.
- If discovered after subsequent pitches that were not batted into play, return the runner without penalty.
- If discovered after a pitch is batted into play, the results of the play would stand.
The first two options assume that another pitch has not been batted into play. They correct the situation without putting either team an a disadvantage, and effectively put things back where they should be. Note that I would extend the defense's opportunity to bring this up beyond one pitch, unlike a standard appeal or protest. Since this is ultimately the umpire's responsibility, I would not hold the teams to the usual "can't appeal/protest after the next pitch" standard. I would consider it a correctible error by the umpire.
The last option assumes that the ball has been batted into play. At that point, the defense has had every chance to speak up and, if they have not, I would consider it too late. Taking runs off the board and moving runners back on base sets a bad precedent and is likely to cause more problems than it solves. It strikes me as compounding the first error, as opposed to correcting it.
Again, this is just how I would personally handle this. There is no specific rule to cover this unusual situation, other than the one that says the runner should have returned in the first place. If an umpire wants to apply rule 10-2-3g and return the runner to third, that is within his authority. When ruling on "points not covered by the rules", there can be no right or wrong answer. If you can sell that call to both coaches without one of them having a meltdown, more power to you!