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The best way to figure this out is to try it, Lewis. Build a master flat for each filter then use one of them to calibrate all the others. If you get a nice featureless result every time then the flats are as good as identical.
Whether dust on the filters will be visible in flats depends on the speed of the scope and the distance between the filters and the focal plane. It's not a problem with my FSQ-106ED but with the Ceravolo at f/9 dust on the filters is all too visible.
Cheers,
Rick.
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