Lightroom 4.4 missing photos
Were you dragging and dropping using Windows Explorer? If so, then LR won't know where they are anymore. Also, I doubt that the missing folders on your hard drive are gone.
Yes,if you move files around that are already imported into Lightroom, you need to move those files within Lightroom not windows. Otherwise you'll need to click on a folder within lightroom and choose "syncronize".