I tried being defeated by the plants in the forest, the puppets, and the bandits in the Old Mine, then searching the rescue locations. In each case, there was nothing in the spot I was supposed to find Emi, since she was still following me. If I got into combat Emi would have the "defeated by Golem" image and would be unable to do actions. I just reloaded a previous save. Enjoying the game! Really wish this and some of the others were available on Steam as well.