Hi Troy
Not really dumb questions – all astro photographers ask these questions at the beginning of their apprenticeship!
A flat field is an image of the “as-used-to-image” optical train so no; you should not change the focus or rotate the camera.
If you change the focus, artifacts such as dust doughnuts will grow/shrink in apparent size.
If you rotate the camera then defects such as dust will now be recorded at a different X-Y position in the flat field image, compared to their X-Y position in the (light) target image.
Then you have other artifacts such as vignetting and gradients, so again, the light image and flat field image need to register precisely. If the flat field is rotated or re-focused compared to the light frame original, when you divide the flat into the light, you will introduce artifacts which will appear as the differences between the rotated sets.
Cheers
Dennis
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