If the quantity of goods changes during the transport process, then you need to make changes to the shipping documents. If you have a change in quantity then you should notify the carrier and have the change noted on the Bill of Lading.
If you have signed a contract of carriage with the shipping company, you can notify them in writing about the change and ask them to change the shipping documents. You will have to pay for this change in the shipping documents. You can contact the shipping company directly to find out the process of making this change.