Hi John,
That sounds like you two have accidently layered those farms. After the current crop is ready just harvest them. Then she will need to delete all the plots on that farm, restart her farms and see if any plots show back up. If they do then she will need to delete those and restart her farms again. Repest the deleting and restarting until there are no more plots showing up.
Then she will be able to replow new plots on the farm and plant.