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Yes, you flats for each filter as the dust bunnies and possibly vignetting will be different between them, and any time you change the camera angle you need a new set too (Unless maybe you are using a smallish refractor and rotating the entire scope in rings to change camera angle)
I normally shoot flats for each session. That is particularly required if you pull anything apart in the image train between sessions as dust bunnies can change session to session.
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