I dont know of any easy to use 3ds hacking tools of that kuriimu
I wasn't talking about kuriimu (whatever the hell that is). Here you said:
Kuriimu exports the logo into a .png file. I used photoshop to make the changes to the logo.
So your photoshop makes changes inside the PNG while saving it, even if you didn't edit it in any way. Try something other than photoshop. Or figure out what exactly does it change (probably PNG header), and change it back each time you want to import PNG back into the game.