This thread started 8 years ago, but there's been recent activity, and I just had this happen to me. I can confirm that the NWD in question in my case is not xref'd by any of the other xref's. It is listed as "nested" and can't be detached.
However, I noticed in my case that there are other nested, orphaned xref's in the drawing. One of the orphaned files also happened to be directly xref'd by the main drawing, and is not orphaned. Like so:
Main drawing
> File 1 (which is found)
> File 2 (which is found)
> > File 1 (path is different than above, and is orphaned)
> > File 3 (orphaned)
> NWD (coordination model)
In the above configuration, the NWD shows as being a nested xref, and can't be detached.
If I detach File 2, which eliminates all the orphans, the NWD becomes "un-nested", and can be detached.
If I resolve the orphaned files by putting them in the folders where File 2 is looking for them, the NWD file is "un-nested", and can be detached.
I agree with @pendean wholeheartedly. If you can reliably reproduce the bug, you have a very good chance that Autodesk will fix it. I've had success with a couple of very annoying and very obscure bugs being fixed when I could provide a way for Autodesk to consistently reproduce the error. I'm not sure what parts of my exercise here are relevant to this bug, but if I can show that this can be reproduced, I will definitely submit a ticket.
