If you want to keep your graphics as they are without silly workarounds that bloat out the sprite file and can potentially lag MUGEN, then yeah.
I switched earlier this week, and it came out perfectly! All I really needed to do in FF Studio was to take the image of the sprite, auto-create a palette for the picture and force-adapt the image to its own palette.
I linked an image that shows how one of my character's ports came out in-game!
Spoiler: My Game Demo's CSS. I practically JUST started on the game, so I simply made a placeholder. (click to see content)