rythm,
Are you asking about uploading a JPG (generated from a NEF) or the whole NEF?
In case of uploading a generated JPG, PM would simply use the embedded JPG in the NEF to generate the JPG it will upload. This embedded JPG is the "current version" of the NEF (i.e., the one that will be shown when you open the NEF with NX2).
In case of uploading the whole NEF, as Kirk mentioned, PM doesn't do anything to the file content and uploads it whole, again leaving its state at "current version".
Hope this explains things a bit.
Cheers,
Hayo