Oh, what a shame!
And that's very odd that there would be that much difference in fading within just a few inches of stitches.
I would check and see if the thread is still sound. Does it break easily? Like with a little pull with a toothpick? If so, you'll probably have to re-do the stitching.
If you go with re-coloring, I would use a permanent fabric marker like Fabrico, Pigma Micron or Identi-Pen - colors made to be safe on fabric.
Good luck! I hope it turns out beautifully!