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You should take flats for ANY time you alter the image train as flats are meant to show up differences and anything you do will change that image path.
That includes any rotation of any part, filter change or sudden movement causing any dust particles to move. This also means flats for anything you use in that session.
Flat darks are also a good idea.
Script in NINA will help automate the process to an extent depending on the capabilities of the light panel.
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