Nikon Transfer 2 would not be my first choice in transfer software, but if it is working for you, OK.
After the files are transferred to your hard drive, using Finder go to the new directory and verify its contents.
Rename the folder if you so desire. Move the folder to its final resting place as needed.
From Lightroom, make sure your import type is "add" to do an in-place import with no file moving/copying.
Your images are not "in" Lightroom. The images are on the hard drive just like your documents. Lightroom references the images by path and filename.
Your edits exist only in the Lightroom catalog. If you want to see the edits outside of Lightroom, you need to export the edits into new image files. Lightroom does not make updates to the original files.
Each of my shooting events are in folders named like yyyymmdd_event_name.
Under that folder are subfolders called "originals" and "exports" containing the respective image files.
Show us a screen capture of the problem in Lightroom. Show us another screen capture of what you see in your operating system.
I want to import the entire folder (as named). I am winding up with a bunch of folders in LR that I don't recognize.
Are you importing into Lightroom using the ADD option? You should be. You should not be choosing the COPY option in this case.
The whole process of using Capture NX and then Lightroom is very inefficient, I would just use LR and import to the desired folder.
Many thanks for the help. You said Nikon Transfer would not be your choice. Can I just use LR for import? Or what software do you recommend? I have Bridge - but frankly I don''t even know it's purpose. Thanks again.
Use Lightroom to import. I have given you a link to a tutorial on this.