Why gimp? Try imagemagick package. It's a great command line image processor.
In your case you can use it like:

convert -negate src.png dst.png

To modify multiple files at once, e.g.

img_path=./path/to/imgs

img_results=./path/to/imgs/results

mkdir -p $img_results

for img in ${img_path}/*;

    do 

    convert -negate $img ${img_results}/${img#./*};

done

The exact method may depend on how you source your paths.

Here's an actual example...

$ for img in ./png-64/*; do echo convert -negate $img results/${img#./*}; done

convert -negate ./png-64/arrow-block.png results/png-64/arrow-block.png

convert -negate ./png-64/arrow-block-rotated.png results/png-64/arrow-block-rotated.png

convert -negate ./png-64/arrow-shrink.png results/png-64/arrow-shrink.png