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They auto delete after a time, or else go Settings-App Clips and delete manually. Convoluted, I know.
 
Settings ➝ General ➝ Usage ➝ search for the title ➝ delete app clip
No need for all of that. App clips appears at the top of the app list. Though it has to be noted that it only appears there when you have an App clip already. Seems to disappear if none installed.
 
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