there's no problem in PI calibration save for the fact that there is a single scaling factor applied to OSC flats. and it isn't really a problem, because the process of flattening an image is simply dividing the flat into the light, which is a linear operation. you can then multiply any channel of your image by any amount and the result is still linear, and if the amounts are chosen carefully, you will undo any cast created by the flat. thus if your image is left with a color cast due to flattening, it is truly a simple matter of multiplying two channels by some factors to restore the balance. nothing is lost in this process. in fact, this is exactly what the various color calibration processes in PI do - compute scaling factors and multiply each channel by those factors.
if you endeavor to make your flats grey, then the process of flattening the image in PI will not change the color balance. however, it's just a fact that all astronomical images need some kind of background neutralization and color calibration regardless of what the flat looked like. the atmosphere, the different transmission percentages of your filters and the quantum efficiency of your sensor at particular filtered wavelengths all conspire to mess up the color balance of your image anyway. so no matter what you do, you can't rely on the colors coming straight out of the camera. you need to perform color calibration.
to ken's question - yes, flats, darks and bias are all applied to the light while the image is still in CFA mode. debayering a flat is really only useful to check what the flat histogram looks like - and generally what you are looking for is that all 3 channels are pretty much exposed to 1/2 the well depth of the sensor at the center of the image. if there is a color imbalance, it's not fatal as described above, but a serious color imbalance can be a problem in the sense that the weakest channel might not have enough signal, and therefore the SNR of the stacked master flat in that channel is poor. this adds more noise to your calibrated frame than necessary.
rob
rob
