What you could try is inserting your edited palette to some free space using GBAGE. This will give you the new, uncompressed palette data in a known location.
Then you simply copy it and paste it over the old, uncompressed palette data you got from the raw dump.
Finally you go to the palette location again in GBAGE and this time hit Load Raw instead of Raw Dump. Now you load up your edited palette and insert it. This should give you your compressed palette. http://puu.sh/pUwjz/bde5f26962.png
Side note, make sure to check “Abort if new graphics/palette are bigger than old” if you’re not repointing, or else you’re likely to break something.