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Chris, I am not sure I understand correctly.
AFAIK Canon EOS 60Da does not have hardware binning. So, if you do 2x2 binning in software (Nebulosity?) and then resize by a factor of 2 (to increase resolution) you will be back where you started... with probably some data loss.
(Also if Nebulosity is doing the 2x2 binning then it must do deBayering before the binning or the colour information will be lost - probably not a problem as you mentioned that the binned stack has colour).
Few suggestions:
Can you check your final images just before stacking, do they have colour. Pick a single binned image and a single unbinned image.
Then separately stack binned and unbinned and see if you get colour for each stack.
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