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Whenever I blend raw files to HDR, some of the dark areas show singnificant amount of noise. It is quite clear that Lightroom uses some of the dark areas pixels from a darker exposure rather from the brighter exposure. See attached 2 images and compare. One was blended in Lightroom (and it is showing the noise) and one I created in Photoshop, using luminosity masks. See how smooth the Photoshop one is
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You might consider posting your source images to something like Dropbox, and posting a link in a reply. This so members can see the originals and give a try at the Merge HDR.