I take the flats prior to the lights with an illuminated cap I manually place on the scope. Unfortunately when doing so, PHD usually loses the guide star. Hence I would appreciate a sequence in this order.
Taking flat frames.
Then start PHD and wait for calibration.
Then pause PHD, do a recenter on the object, then restart PHD.
I’ll ask the obvious question. If you list the flats as the first event in the target won’t those be done first? Alternatively, If you have more than one target, create a flats target that only has s flats event and insert it as the first target.