afaik, you can still play the game if you've copied it. only the one on internal memory will be used for cbhc. in my case, the name and icon didn't change on the home menu, because it's reading the usb version of the game while at boot up, it's reading cbhc from internal memory. I don't know for sure that the game will work, but it's likely it will as long as it's been copied.
Thanks again, I'm definitely going to give it a go once I want to play it, the game in question is Zelda Spirit Tracks which I've never played before, it would be fun to get a chance at playing it later on.