Artifacts after stacking

Could you add the calibrated subs corresponding to the two uncalibrated subs (images 0010 and 0050).
Can you please explain how you are doing your meridian flip?
Do you have a rotator?
Do you change anything in the optical train?
Assuming images 0010 and 0050 are "before and after flip" it looks like a "conventional" flip without rotator (i.e. the star field is rotated by 180 degrees, but the flat structure is unrotated).
 
Could you add the calibrated subs corresponding to the two uncalibrated subs (images 0010 and 0050).

Assuming images 0010 and 0050 are "before and after flip" it looks like a "conventional" flip without rotator (i.e. the star field is rotated by 180 degrees, but the flat structure is unrotated).

You are right: it seems normal. I was on a wrong track.
 
Assuming images 0010 and 0050 are "before and after flip" it looks like a "conventional" flip without rotator (i.e. the star field is rotated by 180 degrees, but the flat structure is unrotated).
That's the point, I think that's the point. Somehow the flat doesn't work out that way.
 
That's the point, I think that's the point. Somehow the flat doesn't work out that way.
No, that is the way it is suppose to be. The meridian flip rotates the whole camera and telescope through 180 degrees, so the star field is rotated. But all the features in the optical path (like vignetteing and dust spots) stay in the same position relative to the sensor, so the same flats work before and after the flip.
 
I still feel like it's somehow related to the flip. The dusts appears to have moved very slightly between frames 10 and 50 and I suspect it's during the flip.
Can you try to do a WBPP run with the frames from one side of the meridian only (the side where you took your flats)?

Another strange thing is that there is a diagonal gradient on your calibrated frames 10 and 50 but the gradient is the same on both frames (darker in the bottom left corner, brighter in the top right corner). If this was due to a gradient in the sky I would expect it to be rotated 180° between the two images so I assume this indicates a problem with your flats.
 
I still feel like it's somehow related to the flip. The dusts appears to have moved very slightly between frames 10 and 50 and I suspect it's during the flip.
Can you try to do a WBPP run with the frames from one side of the meridian only (the side where you took your flats)?

Another strange thing is that there is a diagonal gradient on your calibrated frames 10 and 50 but the gradient is the same on both frames (darker in the bottom left corner, brighter in the top right corner). If this was due to a gradient in the sky I would expect it to be rotated 180° between the two images so I assume this indicates a problem with your flats.
I went back and looked closely at the calibrated frames. I don't see any shadows on 0050, but there is a tiny bit of residual shadow left on 0010. It's subtle, but might be amplified by integrating more frames.
 
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