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when you have saved the bad pixel map, go back to the batch menu and select bad pixel again, this time select "remove bad pixels: BW" and it will ask for the bad pixel map and then ask for the frames to be processed. It will remove the bad pixels and save new processed frames with a badpixel prefix.
Then do what you like with the new frames - remove bias (possibly), deBayer, stack etc - I use the bad pix removal as an alternative to darks - once you have done badpix, I don't think that darks will process properly where the bad pixels used to be.
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