Well, I don't think that's the hardest part. It's certainly time-consuming, and I'm sure it takes at least five minutes to save all the textures and stuff to see a change you've made, but, assuming they're using Photoshop and not Paint, it's quite simple (though time-consuming).
As you can see in the thumbnail below, which is from an early work-in-progress for the title image for a certain
other Zelda game, you can connect the resized textures into the full title image that you see when you boot up the game (I think, when resized, the 'Zelda' logo is around 576x252). Then, you overlay your new logo from somewhere else (scan, internet, whatever.) on top of the old one. The old textures are still there (and retain their exact sizes that are
required to be reinserted into the game) so once you're done, you can simply use magic wand (aka fuzzy select) to select a particular section of your new logo. In this attachment, I've lowered the opacity so you might see what I'm talking about better. The Layers 1-10 are the old, resized textures. Hopefully some of this makes sense...