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My process in PixInsight is as follows.
1) Stitch 2-6 frames together that have both bright and dark areas; this is my template.
2) Set black point, save instance.
3) Histogram stretch, save instance.
4) Revert the template mosaic back to before the black point set.)
5 Use the instances to process each image. This means that every image has the same black point relative to a template. Every image has the sae histogram stretch as well.
I have not yet done a multinight mosaic so I cannot say whether it's work
But I get the same issues as you're currently getting doing them individually as well.
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