Posted by Quick Curly

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Hello, and welcome. I'm not a Mega Man hacker, but it sounds like there might be at least one other palette that you'll have to edit as well to account for those times. In SMB3, which I'm a little more familiar with, there are multiple individual palettes for Mario/Luigi that are sometimes the same matching colours, but they are used in different situations; so if you change one and wish to keep them all consistent, then you'll have to modify them all in the same way.

In case there's anything else to consider for those who might be able to assist you more directly, perhaps a few more specific details would be helpful.
Which specific Mega Man game are you hacking? The first one, or one of the others?
How did you perform the palette swap you already did? With a game-specific editor (like Rock and Roll), or through a special emulator (like FCEUX) and/or a hex editor (like HxD)?
If you search in a hex editor for the values contained within the original palette you modified, do you find any other matching strings? If you try editing one set of values at a time (trying to figure out when they're actually used), do the additional changes fix your issue?

Best of luck. You can do it!

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