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No dont worry about them Stephen. They are part of the darks anyway so when you subtract your darks then its removed at the same time. If you want to remove it from your flats then take longer flats that then require dark frames. Then you remove both at the same time. Not a bad idea to darks for flats anyway for a ToUcam, they are pretty noisy.
BTW I don't know if its the same with a ToUcam but from memory the optimum time for flats is between 2 and 10 sec. Not many follow this though and usually adjust the camera to the light source and not vica versa.
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