HCOTEG61540 - Losses and chargeable shortages on Movements between Northern Ireland and EU countries: Chargeable shortages
Duty on any shortages, where the loss cannot be authorised as allowable by the authorities at the destination, is chargeable to the authorised warehouse-keeper of despatch. The trader will be advised of any shortages when a paper copy of the eAD is returned to the consignee. The trader should notify their officer or the EMCS Helpdesk, and account for any duty on an EX601.
If it can be established, that the shortage occurred somewhere other than the place of despatch or receipt, you will need to refer the eAD to the fiscal authority for the country where the shortage occurred to have the duty calculated at the rate of duty for that EU country.