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From what I have read, you do need to take separate flats if you rotate your CCD using a particular filter. If there is dust on the filter and you rotate the CCD the dust will move.
If you are taking LRGB images flats are necessary for every filter.
You can stagger the roattion every 5-10 degrees take a flat and then median combine for that filter.
Dont forget to do darks for your flats as well.
Mark
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