danosono

Gimp is not a program specializing in pixel art and indexed color modes, so when it saves its rearanging the palette and likely removing unused colors etc to make the resulting PNG smaller. You might be able to find a setting in Gimp's options to have it "not reduce color depth" of PNG images while saving, but if not, you'll need to use a program specializing in editing pixel art, like Pro Motion NG etc. 

If I understand you properly, yes, you'd have to update the portrait manually too. They are separate hand drawn images. The program has no idea if and how you modified one and can not artistically interpret your changes and translate that to the large portrait chest images.

just find the folder with the chest images and edit that to match your new design.
 

It's not simply enough to get the images back into indexed color mode... it must have the color indexes in the same exact order as the unedited originals for the palette changing features to work properly with it.

It would help to use a graphics program specializing in indexed graphics modes (pixel art) as opposed to programs more dedicated to high res full color photo manipulation etc.
It's ideal to use a graphics program that keeps the color palette intact when loading and saving it.
I personally use Pro Motion NG, but any pixel art creation software should work the way you need with the least hassle.