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You can try shooting aperture priority mode as well as auto ISO. I think also there is a menu step where you can program the minimum ISO steps. Make sure that is set to the lowest step.
Also when setting auto ISO don't forget it also asks for minimum shutter speed so set that thoughfully. Too high and it will give the camera a problem when it gets dimmer. Too long and it will overexpose before sunset. So you set the aperture to suit.
I have done a sunset to dark time lapse with D800E and it was relatively smooth. There is also a deflicker plug in from Granite Bay Software. Not sure if it works with Nikon and jpegs. You'd have to check their site. It works in Lightroom.
Greg.
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