As the app duplicates variants, first it is necessary to remove all the extra variants from the app to make sure that any extra information is removed.
Make sure that all the variants are unchecked. Press "Save Changes". This will remove all the extra variants stored within the app.
Remove the app by clicking on the bucket
Simply confirm the uninstallation and you will be all set. Please NOTE: This operation can only be performed by the store owner. It will automatically cancel the billing for the app and no future payment will incur.