You can change down payments by changing the document or the line items in a customer, vendor or reconciliation account. You may have to change the document or line items to remove a payment block or change the due date.
You can find further information on changing documents in FI - Document Posting. Here, you can also find out how to change line items.
When changing line items for down payments, however, you must select With special G/L transactions in the initial screen. Otherwise, the system does not select the down payments.