ok it's more clear now and it's quite an odd behavior that I didn't experienced when I was using sky flats.

But increasing the tolerance should lower the chance of hitting the threshold during a entire session of flats (at least for each of the filters).
I mean, if you set 16000 +/- 4000 the chance that all the 40 (maybe better to lower to 20) flats ADUs are in the 12000-20000 range is greater. So no need for 'cycling'.

And having flats with a wide range of ADUs is ok as long as they are normalized during integration.

I see that this is not a solution to your issue but more a workaround to avoid it.

Ferrante

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