Actually, I don’t see a way to do it properly because a custom line item isn’t really a product. In some cases, it may be an option to delete the entire order and recreate it with the properties. We didn’t have that option, so our workaround was to put the data on line item discounts on the description property using the orderEditAddLineItemDiscount mutation.
It’s worth mentioning that this all could have been avoided by having validation on the front end.