33 hours of data. I look forward to seeing the result. There are a few ways of tackling the situation, but before we delve too deep. Run your subs through something like CCDInspector or another data interrogation algorithm... your making an assumption that all 100 subs are perfect. Its less than ideal if you combine premium data with mediocre. You could be left with 80 subs ofter the data reject. A good indication is to evaluate FWHM of each sub.
As you indicate, work in data sets. 12 subs usually provides ample information for outlier pixel data rejection algorithms. Once you've got your 8 or so combined subs, combine them again. I've heard of imagers doing the initial combine using a lower sigma reject value to keep some outlier pixels in the data. These are then addressed on the second combine pass. What you want to avoid is an aggressive sigma reject on the first pass. Too aggressive and the algorithm has the potential to mistake data for noise. Clearly, not good.
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