To be on the same page and in case I mis-understood you, don't put the stars back from Ha image. Remove stars from Ha image and run the HaRGB or NbRGB script with combined RGB. This way RGB stars will be preserved and not be ruined by stars from Ha image. I have been planning on trying this but I have been too busy. I will try removing stars from Ha image with PixInsight and see what happens this weekend if nothing else interferes with my plans.
As for processing individual channels like DBE or Linear Fit, I am not sure and I think it's entirely a personal preference. IMHO, running DBE on individual channels or combined RGB may not make much difference but try it for yourself and let us know. Personally I use DBE on combined RGB and Luminance separately but I have not yet tried DBE on individual R, G, and B channels.
Also, after combining Ha with RGB using HaRGB script, next I run DBE. I haven't yet tried DBE on Ha alone. If you run DBE on Ha first, then you might want to run DBE on combined or individual RGB before HaRGB combination. Just make sure the timing of running DBE is done correctly.
For Linear Fit, I have seen Linear Fit demostration using non-linear (stretched) images but not on linear images. The word "Linear" in the title "Linear Fit" may be mis-leading. Once again, try it for yourself using both linear and non-linear images. The results may be enough to tell you.
Peter