Usually, they recolor like this:
1. Select the texture area to be recolored using the lasso tool;
2. Find the "hue/saturation" tool in the graphics editor (in Paint.net, it's located in "Adjustments," if I remember correctly);
3. Open it;
4. Drag the "hue" slider left/right until the desired shade is achieved;
5. OK.
But recoloring each pixel would be a nightmare. :)
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