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1. Why would PKHeX want to be any different than how the games work? You can always try it and see -- you'll see that PKHeX retains everything the same way the game would. 2. You don't need to do each step one at a time. PKHeX chains all the conversions together for you. 3. You shouldn't need to override it from the default, so Yes/Cancel is the correct option for you. It's only useful for advanced users just wanting to inspect data unmodified. Trades update things and ensure it ends up in a legal state (like traded eggs or memories).