How do you copy a desmume and pokemon soulsilver game without restarting your game?

I couldn't play my pokemon soulsilver game on desmume without moving both of them from my flash drive to my desktop. So I moved it to my desktop and started to play my pokemon soulsilver game. Unfortunately, my game wasn't saved from my flash drive pokemon soulsilver game. How can I copy desmume and pokemon soulsilver from my flash drive to my desktop while saving my pokemon game? Thanks a bunch! I may be a girl, but pokemon is my life!! ;)

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