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Hi Lachlan,
It does look like your flats don’t match and have over compensated as you have said. I normally don’t touch my focuser after my imaging session before taking flats. There’s just to much risk of something moving or introducing human error. I simply use the last position of the focuser for my flats. In fairness I also take my flats the next day so due to expansion they’re never going to be absolutely perfect. I don’t see any issues when I do it this way though either. I use the ASIair too.
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