Ok I have half an answer for you. I went through the same thing and recovered 1 TB files. Trouble is I have forgotten the fix.
Go to Terminal in Utilities and show hidden files by typing the following:
defaults write com.apple.finder AppleShowAllFiles 1
Now look at the drive that has the problem. You will see your original files in hidden mode and you will be able to explore them. Oh wait let me try something...
Ok I have the full answer for you and here it is:
Go to Terminal in Utilities and show hidden files by typing the command above. Go to the drive that has turned your folder called XYZ into XYZ.exe
Make a new folder called XYZ2, drag all the files from the hidden folder into the new folder. Delete the now empty folder and the .exe folder and your drive will be as good as new.
I don't know how to hide all hidden files again.
Cheers from Pakistan!