Usually I process as the images come down after several nights. Working on a bunch of M53 images I had calibrated I went into the Star Alignment process and listed all the luminance images I had calibrated, about 60 of them. I opened each one by double clicking on each one, one at a time, used STF to examine them and then decided then as to whether I'd use them or not. If not I'd double click the check mark making it an "X" to exclude the image from the usable group. At that point I realized that I had forgotten to use Cosmetic Correction process to remove the hot/cold pixels and needed to do that first. So here I have a group of usable images listed in Start Alignment process that I needed to have in the Cosmetic Correction list.
My usual process flow goes calibration/cosmetic correction/star alignment/image integration. I've tried using the script to cull for best images and always seem to get some that just aren't suitable for the image and end up degrading the final image. So I'm back to my old fashion look and see before adding routine. I even manually calibrate my images as the BatchProcess doesn't, at least the last I looked, have a way to use the proper E/W flat for those of us using rotators. I hope this makes sense. I guess I really need to add an additional step of calibrating and then opening each image to determine it's quality and then saving as a separate group. But that means doing each one at a time taking a substantial amount of time on large stacks. Unless I'm missing something obvious.
So in this case I had calibrated the images, loaded the saved images into Star Alignment, opened each to check for usage, gone through the stacked and marked those unusable with an"X", and then realized that I needed to run Cosmetic Correction before aligning the images. Getting the checked images copied over to the CC list to run was where it would have been helpful rather than listing them all again and opening each or trying to go through the long list and adding each working from the alignment listing. Convoluted I know and a misstep on my part. It just got me thinking as I'm sure this won't be the last time for me.
Hope I made it a bit clearer.