Check the game manual to delete the save.
Don't get it you mean to delete the save of my orignal game?
Or can't I just try to use a different header.
Changing headers does that. To prevent this make sure to backup the save using savedatafiler
To be clear I want just to transfer some pokés to modify.
How do you want to transfer them? If you install savedatafiler you could export your save to you sd card then move the save to your PC and edit it via PKHEX and import that save back into your game.
Don't get it you mean to delete the save of my orignal game?
Or can't I just try to use a different header.