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issue isn't about changing to colour, if you do the calibration will not be accurate! and you most likey will loose data which is bad!
Just follow the premise of
All photos to be in RAW not debayered
Take your photos
Take your calibration photos darks flats and bias
Apply your calibration photos to your lights
Debayer your calibrated images
Register (align) your images
Do all your noise rejection
stack your images
output them to a TIFF file
open in your fave processing software.
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