I also routinely scale my darks even though they are done at exact temperatures.
I subtract a bias from the master flat when applied not when making the master flat.
I also check the callibrations are working as I am imaging rather than assume they will. I tend to trial and error it a bit as often the calibration does not work that well until I get it looking right.
To add to the complication my FLI cameras have a slow download and a fast download speed with different read noises. So its usually not a problem but I have to make sure if I was using the faster download speed to speed up focusing I remember to switch it back so my calibration files match.
Callibrating astro files is a bit touchy especially now almost every scope has a reducer or flattener.
Greg.
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