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For blending and this is not the only method, but one I use; I blend the Ha to the Lum layer in photoshop and then do a combine in CCDstack with the colour RGB.
Sometimes it is good to blend the Ha with the individual colour frames too.
What ever choice you make the colour or lum must be the background layer and the Ha is blended over the top.
The colour shift or what you are seeing could be the colour settings you have in your photo editor. I use sRGB IEC61966 for the most part. Sometimes using Adobe RGB 1998 is a require colour setting. Each has subtle hues and tones. If you are using other ones to this then that could be the reason for the changes you are seeing. Otherwise colour should remain the same on upload.
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