To my knowledge, it is best not to move the camera and take flats exactly at the same orientation and focus as it was for imaging session. Also, if signal in flats is too weak, software won't correct properly for uneven illuminations due to optical imperfections. I have found through experimentations that I need to reach about 2/3 of the maximum values for pixel wells in the flats for them to work properly. I hope it helps a bit
Regards
Suavi