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I found the workaround below, but it is unclear which amount of vAT should be filled in in step 3. A ‘0’ is not accepted.
For now, you will have to do this via a ‘workaround’. I will type it out here.
Add the document twice.
The first time, enter the document as you would normally, entering the full amount, recovering the vAT, and so on.
Then you enter the second upload and in step 2 (basic information) you select “expenses are a credit note”. Here, you also select that you do not want to include this expense in the vAT declaration (only available for subject to VAT businesses). Then you enter the amount paid by the SME portfolio as if it were a credit note, but in this second document only for the amount paid by the SME portfolio.This is why it is a bit of a detour: the first document is the total amount for the costs in your accounts & recovery of vAT via your vAT declaration. Using the second document (which you do not include in your vAT declaration), you enter a portion of the costs entered in the first document, because this portion has been covered by the SME portfolio.