Download and open "fix_corrupted_nef_win.zip", then move the "fix_corrupted_nef.exe" application onto your hard disk.
Drag and drop the corrupted NEF files and/or folders onto the "fix_corrupted_nef.exe" application.
A command window should open and prompt with this message:
"Bit depth of compressed images (12 or 14) [14]?"
Type either "12" or "14", then press RETURN. If you don't know the bit depth of your compressed NEF images, or if you have mixed 12 and 14-bit compressed images, or if you have only uncompressed NEF images, just type "14" (or simply press RETURN). If this is wrong for some images, you will not be able to open the fixed images (but you can delete these and re-generate them with the other bit depth later). Note that this number is ignored for the D3200 and D5200 since the NEF bit depth can not be changed for these cameras.
The application should now run and create a "fixed" folder beside each of the original NEF images. This folder contains the fixed NEF images with the same names as the originals.
Verify that you can open the fixed NEF images. If you can't open any of the images, delete them and go back to step 2, but this time select the other bit depth in step 3. (Only the images you deleted will be re-generated, the others won't be touched.)
With any luck, the mess caused by the Nikon software is now fixed, and all of your NEF images are now restored!
If you are feeling so happy that you absolutely must send me a donation, this can be done from the ExifTool home page.