You will have to redo OW palettes.
I CALL BULLSHIT.
If you go to File > Palettes > Extract Shared Palettes from ROM, it's possible to save your overworld palettes. Strangely enough, they use the same .PAL extension that Lunar Magic uses for your custom palettes in YY-CHR format.
Make sure to delete your backup when you're done or keep it up to date, because if you try to restore from it later, it will inadvertently overwrite colors that you may have changed. Something I learned the hard way!