I think it has something to do with the all the overworld pokemon being shiny. Normally without any cheat codes your pokemon wont auto battle shiny pokemon, it's built in the game so you wont accidentally kill shiny pokemon. Try disabling every cheat then starting the game without them, save...
Check the settings, theres an auto ignore learning moves option. Then check in the summary-moves panel if your new moves are in there when you open the relearn moves panel.
Anyone tried breeding Hacked male/female Koraidon with hacked male/female Miraidon and have eggs? I could try, but I don't want to waste time if someone already tried/knows what's gonna happen.
Somehow I got it to work, I copied the CE settings here
I progressed through the game first after you can ride the legendary, maybe thats a variable you have to continue story first