I have used CNX2 for years, but have never saved in a NEF format. When I do (after cropping and straightening in NX2) and then reopen the saved image in PS/CS6 (starts ACR) what appears is the original NEF image. Why is this happening? Can the NEF not be saved in a modified configuration? And if not, why is the NEF saving option even offered?
The image data is not changed by CNX2 (of any other software that edits the NEF). CNX2 adds the edit steps to the meta data in the file and updates an embedded JPG in the NEF file to reflect the latest edits. If you save the NEF and then run CNX2 again, CNX2 retrieves the image data and applies the latest set of edit steps. Thus subsequent runs of CNX2 will let you pick up where you left off. CNX2 will also let you save versions of the edit steps and recall them by name, so that you can have multiple editing scenarios in the NEF meta data.
Most other software is unable to interpret the CNX2 edit steps to render the picture and thus will start from the never modified image data in the NEF.
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The edits that you make in CNX are saved with the NEF as a set of instructions that the software uses when displaying on screen or saving to another format. Those instructions are CNX specific. ACR/PS/LR cannot read them, so you continue to see the base file.
This is why editing a NEF in CNX or VNX is non-distructive, the original data isn't modified, only instructions are added and a JPG preview and/or thumbnail of the edited image is embedded in the NEF.
Every raw program stores its edits differently, including NX2, and they're not compatible with each other (with some exceptions within the same brand of converter). NX2 stores its edits in the NEF. If you want to re-edit your NEFs originally edited in Capture NX2 at a later date (which makes sense), you'll need to save them in the NEF format and then use Capture NX2 to edit them. Photoshop can't read the Capture NX2 edits (and neither can ViewNX2), but you can save the results as a TIFF and then open that file into Photoshop. If you want to edit your raw files within the Photoshop environment, you'll need to use ACR throughout the process.