I am new to SX OS, but when I have wanted or needed to do this, I would unmount that game, then through the Switch UI, "Delete Software" as it does not delete your saves. I should add that I primarily use XCI files, and if your original game is an NSP it would likely remove the game.
Is there any downside to using this approach with XCI files? Sorry to piggyback on your thread but I have been wondering as well.