A deposit created from a received order is always item-free (without line items). Therefore, deducting it from an invoice is only possible from the other direction — first creating an invoice with line items for the relevant amount, and then deducting the deposit (via Services in the detail of the given invoice).
The second option, which is likely more user-friendly, is to create an invoice directly from the received order. If a deposit has already been created for that order, it will automatically be offered for deduction when you attempt to create an invoice (tax document). Upon confirmation, an issued invoice will be generated with the relevant line items and the corresponding deposit deduction applied.