I've taken a look at your linked image. The problem is that the following crucial information is missing from the NEF maker notes: NEFCompression, ContrastCurve, LinearizationTable. Presumably this happened because the maker notes were copied from a JPEG image, which doesn't contain this information.

The best you can do is to copy the makernotes from an original NEF image to replace the makernotes in the affected NEF's. This can be done with the following command:

exiftool -tagsfromfile good.nef -makernotes bad.nef

After this, most of the maker notes of no longer correspond to the original image, but you can recover what you can from the JPEG version of the maker notes by executing this command afterwards:

exiftool -tagsfromfile bad.nef_original -makernotes:all bad.nef

This will copy the existing individual maker notes tags back again. (Note that the 2 steps are necessary because maker notes tags may not be created individually, so copying the entire MakerNotes block was the only way to get the necessary tags back into the image.)

When you are done, you should have a usable NEF image, although the linearization may be slightly different so the levels might not be quite the same as they were originally.