It counts as a pirated copy, it won't move when you transfer (unless the console you're talking about was the target).
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Is it running A9LH or menuhax? If A9LH, follow
https://3ds.guide/a9lh-to-b9s and if menuhax, then uninstall menuhax (boot to sysNAND, change the theme), then follow
https://3ds.guide/homebrew-launcher-(soundhax)
In both cases you should later follow
https://3ds.guide/move-emunand to get rid of your emuNAND (will only cause you problems and not help anything) then follow
https://3ds.guide/finalizing-setup to get all the latest homebrew.
I don't think Cakes is compatible with the latest firmware version.