I just add, that cosmetic corrections is a method to repair bad pixels in the RAW light images. It should be applied to every image individually. Of course you need to develop the template that identifies the bad pixels (also can use the master dark in the CC routine). Remember, the purpose of CosmeticCorrection is to repair individual pixel defects that lie in the camera sensor. You identify those pixels by the (X,Y) coordinates. So apply the CC before shifting pixels around by something like image registration.
Maybe this is not how most imagers do it it, but after CosmeticCorrection I select one crisp image then use the StarAlignment procedure to register all images (R,B,G,Ha,...) to it. Then I use the procedure ImageIntegration to make the individual R,G,B,Ha,...stacks. I prefer this to using BPP, but the same idea, I guess.
Alex