Processing XCF files in batch

[Ofnuts]

I don't see such a problem. If you are talking about the partially transparent area in the arm (covering the thumb), then the layer color has been replaced. However, since the layer is partially transparent, the color picker will report the blend of the color and whatever color is below if the Sample merged option is checked.  If you uncheck the option, you get the actual color in the layer.

Here is what I see (I use the Pointer dialog to explore the image, faster and more options than the color picker)