When running a sequence and i have the image history open i notice the auto focus position over the night drops 10 points or more as temp drops my question is when i come to do my flats for the filter in use what focuser position should i use? or should i just put roughly the middle of the two numbers.
Use the focus for the temperature at the time you do your flats. An average focus position from previous temperatures would not be the best focus.
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As long as you dither you will normally be ok without thinking about temperature changes, if you don’t dither there might be problems, but it depends on your setup
I’m not sure I understand what dithering has to do with taking flats.