Palette issues editing portraits and sprites

Hi all,
Brand new to modding FF6/3, forgive noob question.
Veteran unix admin, non-noob to general CS concepts.

So what I'm trying to do as a learning exercise is to simply swap the graphics for Leo and Cyan.

I've used FFSE Final Fantasy 3 Sprite Editor V 2.11 to do the swap of the portraits since no other editor seems to have this ability, however doing so screws up the palette for all kinds of things.
I've used FF3usME 6.8.0 to edit the walking/battle sprites without any trouble, but doing the portraits seems to be the only useful feature FF3usME lacks.

Anyone have advice on the best way to safely edit character portraits?

can't say i've ever come across an error by simply importing a portrait, just export them then reimport them, should be as simple as that.

I tried going from scratch on a clean rom and didn't run into the same issue, so I'm going to write it off as user error - maybe I screwed up the palette itself.

However now a different issue has cropped up doing the same operation (switching cyan and leo) with the sprite default overland palette reverting to the originals (cyan, now leo gfx, going to palette 4 and leo, now cyan gfx, going to palette 0) when viewing the rom with FF3usME

i'm not sure why you're trying to switch their places in usme to begin with tbh, the pallets are hardcoded to the respective characters (leos slot will always use pallet 0 and cyans 4) so that will always be the case. Instead what you might want to do is just change which sprite is assigned to the character via eventing.

Leo, by default, doesn't have a chocobo riding sprite, so it would glitch out with portions of Banon. He would either need to expand the sprite in free space, or change the respective sprite sheets. So this isn't a bad approach. Especially for new modders.