Title suggests the issue. I imported a thing for my ROM using the secret bitmap pasting trick and the palette is correct to the graphics but only on the editor itself. When I load it into SNES9X, I get different colors, presumably a different palette. I'm not good with this so bear with me.
And no this ain't a April Fools joke or anything I'm making a vaporwave based hack lmao
Edit: I'm dumb and figured it out again, thanks with some help. Just moved the palette to one that wouldn't be overwritten.