Weird Situation

[MOofficial]

This is something that is probably never going to happen, but what would be the ruling.

R1 on first, Batter hits a long fly ball down the line, R1 is going with the hit and run, R1 does not quit running even though it is fly ball, makes it all the way to 3rd. Umpire announces "Foul Ball" R1 decides to go back to second not first, no one realizes where she is at. Players are ready to go on, pitcher pitches the ball, umpires do not realize what is going on, Batter swings another time hits a line drive to the outfield, R1 scores, ball game is over with the run. Wait coach comes out and says that R1 did not go all way back to first on the foul ball, she stayed at second. What happens, I'd assume you would have to redo it all, putting the runner back on First.