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Debayer is what they call demosaic in Nebulosity.
Your monochrome FIT file contains a bayer matrix. Let's say:
RG
GB
Your whole sensor would be:
RGRGRGRGRG..
GBGBGB..
RGRG..
GB..
..
You get the idea. So your whole frame contains the color information embedded in it. 2Gs for 1 R and one B. Debayering or demosaicking means get all the reds, all the blues and all the greens (combined) in three separate files. Then those three files are recombined to make your RGB channels.
What is important to understand is that your flats, darks and bias contain a bayer matrix as well. So if you debayer your subs you have to debayer your master flat, dark and bias as well to calibrate them.
If you don't debayer your subs, then you must not debayer your flat, dark and bias masters. There is no point debayering before calibration. It's just more work. Hope this all makes sense now.
Another very important point is that you must not crop, scale or register/align any file containing a bayer matrix. The reason is obvious. You modify the bayer matrix.
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