This happens in both Lightroom 4 and 5. I created a smart collection to find all the Portrait photos. In library grid mode while I was still in the smart collection I selected several of these and changed the orientation to Landscape. As expected they were removed from the smart collection. I went back to all photos in Library Grid and the thumbnails in the grid for these photos disappeared. The BOX in grid view for the problem photo is where it is supposed to be with all the badges, flags etc that are supposed to be there but the photo is not. I can see it in the navigator or when I switch to Loupe. I can also get it back in grid view by rotating. When you restart lightroom, the thumbnails reappear.