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You could.
But, it would be even better to process the first lot separately, then, the second lot, and so on.
Night one lights - night one calibration (darks, flat lights/darks) = night one reduced lights.
Night two lights - night two calibration (darks, flat lights/darks) = night two reduced lights.
Then, combine reduced lights using your favourite algorithm (kappa-sigma, SD clip, etc.)
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