I have a few files(pictures) that say they are corrupted or that their directory is messed up. The thing is my camera shows a thumbnail of the picture so I figure the file is not corrupted but instead the directory is messed up.

Anyone know the proper way to go about either rebuilding or having something rebuild the directory on the 4 files?

you could try a program from Ontrack, called Easy Recovery Professional. I've had good success with it.