I have had the same problem, suddenly one day, thousands of item missing from the folders. All folders in inventory but nothing inside them. I have tried everything suggested, even took out firestorm and reinstalled it and still they are missing. went to Pooley to try that and nothing.
I think this is a firestorm issue and someone needs to look into this. I installed SL 4 viewer and items are all there. So it has to be something with firestorm.