As others suggest, I always save the edited NEF before converting to a JPEG. It may be as simple as saving it in View NX2 for a minor edit or it may be something more involved in Capture NX2. I typically don't use versions very often. When I do it is usually for B&W conversion which involves several steps.
One tip that works for me. I take all JPEG conversions for web posting (resized and sharpened) and put them in a single folder - Web Posts. I find that I often use these images more than once, and having them quickly accessible is quite convenient. I don't share lots of images from a shoot or trip - usually 5 or less. And I do purge some of the older images into an archive. These images are typically used for my screen saver or copied to my iPad ad iPhone.