Nod to file recovery.
by R. Proffitt - 4/9/13 9:34 AM
Let me lead with this is not a cure to undo the damage. At this point I would copy off all the files and folders I can THEN and only then, go get RECUVA to scan the drive for other missing files.
Copy these files out with RECUVA (it's free and with so many tutorials I see no need to mention more than the word RECUVA) and then start over.
FAT is dangerously easy to corrupt so don't feel bad or that you did the damage. It's an old thing from over 2 decades ago and untrustworthy.