Sorry, I don't understand what you're suggesting.
I plan to collect flats at the end of the night after I've collected all my lights from an autorun session. I have a filter wheel and I'm automatically changing filters during the autorun. After each filter change the EAF auto focuses and finds the best position for optimal focus. What I don't know is the EAF focus position per filter, if I had this, I can easily take flats.
So in pictures. Take this value at the time each image is taken...
And put it in the fits header.
I'll then manually go through and take flats after setting the EAF position per filter, unless that can also be automated. 🙂