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You may be able to get away with a single set of flats depending on how fast your scope is and how far the filters are from the focal plane. A faster scope will throw dust motes further out of focus as will greater distance from the focal plane.
Try a test... take flats with each of your filters and see how good a correction you get when you apply a master flat from one filter to master flats for the other filters. If you get clean, evenly illuminated results then you don't need separate flats for each filter.
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