Just an update:
I have circumvented this problem by editing the palette directly, without adding
channels or anything overly complicated.
Here's what I did in case other people experience similar issues:
I modified the color with index 16 from #878787 to #898989 (editing html
notation). This changed that color everywhere in the picture.
Then I edited the index 255 color's html notation as well, from 875487 to
878787, which again changed the color everywhere to the correct value.
After saving the file, I can now freely edit and export it in GIMP with no
further issues, the game properly recognizes all the colors.

-- 
Blasphemous (via www.gimpusers.com/forums)
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