You mean the 'magic pink' color behind a skin? (html code: FF00FF)
I am not sure with gimp, never have worked with it. Try this:
Make 2 layers with the skin on it, take the magic wand tool and select the pink on the second layer, now delete the pink, you should only have the skin on the 2e layer, and the magic pink on the 1st.
Now you can recolor the skin to what you want.