to the best of my knowledge, no - your settings will not be overwritten if you have the "auto" set On as default. when you adjus the NEF file, then convert it to a DNG it "bakes" the settings into the file, so when its opened as a DNG all the settings, metadata, labels etc are preserved, the same as the NEF file, but without the need for a sidecar XMP file.
Hope that helps

Graham