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Sounds like you're confusing mono camera techniques and DSLR techniques.
If you use a Ha filter on a DSLR, you're still capturing RGB data, it's just that the majority of that data is in the R channel because that's what the Ha filter is letting through. G and B data will just be noise.
Do you have a colour image and want to use Ha as a luminance layer? If so, just put the RGB image in one layer, the Ha in another. Set the Ha layer blend mode to luminance and the RGB one to colour.
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