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I'm looking at the manual and there is a setting for Noise Reduction Long exposure". The factory setting is set to On which is where I have it. This does affect raw images. Then there is a setting for NR in JPG and that factory setting is set to Low, which is where I have it even though I don't shoot JPG

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LENR is something quite different from "normal" noise reduction.
It uses a second exposure to detect  and correct variations in pixel sensitivity during long exposures at raw level. This removes noise that cannot be removed by other methods and will not impact resolution.
Normal noise reduction smoothes the noise by algorithm which will impact resolution, sometimes severely, and works on JPG images and during postprocessing. As JPGs are derived from raw data LENR can be used for subsequent JPG  output as well.
AI noise reduction uses AI (obviously) for replacing data and is done during postprocessing.

In general it is best to use LENR (unless you are in a hurry shooting) and save further noise reduction for raw postprocessing, as the computer is more powerful and sophisticated than the camera.

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I came across some of my images in JPG-DNG from SL3

I have to say the noise from the JPG was very dominant and made me reflect twice on whether it was a setting error or not. It was very strong at normal settings even at 6400 ISO. the DNG file was totally fine.

The JPG are much noisier than any of the images I have processed myself with NR and sharpening turned off. My conclusion is not to use the JPG for final work in most cases.

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