Recoloring a tga file can be tricky, especially if the image isn't square or rectangle. What I do is just copy the image only and paste it as a new image. Then recolor only the image and thereby leaving the transparency alone. If you recolor the new image and copy it back to the position in the TGA it should work. It worked for me. Your way, the image did disappear. You can also make the images from scratch and save them as a png and load the new images you created, and SS will create the tga for you.
