I replaced none shiny Zorua with shiny Zorua, they have different ids, so basically I did.
If you want to replace one yourself it's simple once you know what script to edit.
1) Open the rom in sky temple
2) Find the ids of the pokemon you want to replace and the pokemon you want to replace it with. You can find the pokemon by searching the name in sky temple. The id will be next to the name, male and female have different ids. You might need to add/ make more portraits if the pokemon you want doesn't have a full set, not sure tbh.
3) Go to "Script Scenes> Scripts" and hit "Open Script Engine Debugger". This opens the debugger in its own window.
4) In the Script Browser window search for "S02P01A"
5) open "Acting>newtest3.ssb"
6) CTRL+f the id of the pokemon you want t replace, then paste the id of the pokemon you want instead in its place, there should be two lines with the id on to look for, but you can keep using CTRL+f until you've found them all. You'll see a line near them with text that reads something like Is "[CS:K]Zorua[CR] who you want?" You'll want to change name in it too I assume.
7)Save the script and save the ROM and you should be good to go, just reject whoever the test gives you select the one you added manually.