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Josh,
You may be able to get away with a single set of flats but it will depend on your optical train and how fussy you are. If you have a fast scope and the filters are far enough away from the CCD then any dust on the filters may be so far out of focus that it isn't visible. If you have a slow scope or a filter wheel that's close to the CCD plane then you may find the flats for each filter are significantly different.
You can always perform a test and see how much difference there is between your master flats. If you divide one master flat by a different master flat you will get a mostly featureless result if the flats are similar.
Cheers,
Rick.
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