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Palette Swap replaces each color of the active Color Palette with the color in the same slot of another palette. Use it for character skins, team colors, or color cycling, without recapturing the source. Palette Swap needs an enabled Color Palette in the same profile. It runs last, so palette-colored lines are swapped too. A character with its original palette, then swapped to a green and a purple match palette

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Settings

Under the fields, a mapping strip shows each source slot (top) and the Match color it becomes (bottom). Colors that are not in the source palette pass through unchanged, and transparency is kept.

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Make a recolor

1

Get the source palette

With an Auto palette, click Export on the Color Palette to save it as a Pixelate Palette. With a Custom palette, you already have it.
2

Duplicate and recolor it

Duplicate the palette asset in the Project window (Edit > Duplicate), then change its colors slot by slot. Keep the slot order: slot 3 of the copy replaces slot 3 of the original.
3

Assign it as the Match Palette

Add Palette Swap and assign the copy. To recolor one asset only, turn on the Match Palette override in that asset. See overrides.
To edit the Match Palette right here, click Edit Match Palette. For an imported palette file, Create Editable Copy makes an editable copy first; for an image, Create Pixelate Palette does.
If the palettes have different lengths, slots wrap around the Match Palette. When the Match Palette is shorter, some Match colors are used by more than one source slot; the Inspector tells you when this happens.