Hi Mike!
The flats, with foils or Skyflat, usually have another Color imbalance based
on the Input medium. The idea is to neutralize the imbalance of the Input medium (Sky, foil).
The lights calibrated at the beginning with neutral channel masterflat will be Color calibrated later on.
I preprocess the masterflat before to keep them as RAW gray flats showing the histobumps together instead of separated.
And use the treated Master for calibration of lights. No preprocessing of the raw lights before calibration.
Gerald