They come back as soon as I click the Walk icon to stop using the "Add to Animal Building" tool. They're just sitting on the plowed fields, perfectly visible, until I enable that tool and they magically disappear. The moment I stop using the tool, they come back, and I can move them to the animal buildings by clicking on the individual animals.
Plant a crop on that farm, then hide the crop, reload the farm and see if you can move the animals then..