I recently moved my photos from one HD to another. I didn't change anything about the file names, just changed the location. Now, when I did this a few days ago, everything worked fine, but now it's making me go through each photo, one by one. ANNOYING!!!
DJ has you pointed in the right direction.
LR understands the difference between missing images and images in missing folders. You need to fix the missing folders first, if you have any.