I am running into this problem where removing a green screen using GIMP messes up the colour balance of the elements in the image.
To recreate this simple problem I chose an image with an alpha channel (image on the left) and I added a layer below it with a
#00ff00 fill (image in the middle). I then merged the layers and applied "Colour to Alpha..." using
#00ff00; the result is the image on the right.
As you can see, the blue and red dice from the original image are quite accurate (perhaps because they have no green component on their colour composition?), but the problem arises for the two green dice: you can see that the one on the top right becomes grey...
Is there a proper way to deal with this? Thanks.