NEF files not showing in file explorer

Nikon Transfer is known for corrupting raw files, and I see in the metadata that you used it @sotherbee. Avoid it like fire.
To repair these raw files, http://owl.phy.queensu.ca/~phil/exiftool/fix_corrupted_nef.html

If you’re looking for a libre program for uploading raw files from camera to PC and managing them and metadata, try digiKam:
https://www.digikam.org/
http://download.kde.org/stable/digikam/digiKam-5.1.0-02-Win64.exe

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