If you have three items in the order, but only two of them get shipped, you can send an adjust order request with the two remaining items in it before or after the Create Invoice request.

This request accepts the desired state of the order after the adjustment.
The order can be adjusted in the state:
- confirmed - the amount can be decreased or increase
- partially_shipped - the amount can be only decreased
The increase of the amount can be declined by risk engine if the buyer limit was exceeded. In case of decline the API will return 422 error.