If only a few colors change, then you would just have to go back and change those colors to harmonize all the screenshot together. If the whole screen experiences the color change like some sort of global lighting effect, then it becomes a matter of taking a ton of screenshots of each area and assembling together those which share the same exact colors.
Considering how long it took to harmonize a total of two colors for some Sonic CD levels (we're talking going back and altering the colors of several hundreds of images), I can understand that people don't want to take this stage on.
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"With the first link, the chain is forged. The first speech censored, the first thought forbidden, the first freedom denied, chains us all irrevocably." [...] The first time any man's freedom is trodden on, we're all damaged. - Captain Jean-Luc Picard
Current projects: Sonic CD (Sega CD), Mega Man V (GB), Mega Man Zero (GBA), Battletoads (NES)