Vendor down payment with input tax

Dear Expert
My client receieves down payment with input tax, to meet their legal requirement for VAT filing, they have to book entries as below;
When receieving down payment with input tax:
Dr. Down payment
      Input tax
  Cr. Bank
When receiveing vendor invoice for remaining AP amount:
Dr. Expense
      Input tax
  Cr. AP (remaining amount)
Then clear down payment by expense
Dr. Expense
  Cr. Down payment
They do in this way, because input tax in down payment and input tax in remaining AP invoice should be listed as two items in their VAT report. And intput tax in down payment document is with reference field which is different from reference field in remaining AP invoice, and reference field is also one mandatory field in VAT report.
In this case, I can not use SAP standard T-code F-54 to clear down payment. But when I tried to create a manual JV to post entry with Dr. Expense and Cr. Down payment, it's OK, but then when I used F-44 to manully clear down payment doc by manual JV, I got problem because the amount in down payment is down payment amount + input tax amount, but the amount in manual JV is only down payment.
Does someone have a solution?
Thanks,
Nicole

Nicole,
Which country is this requirement for?  As far as I know, there is no tax incidence on downpayment.  Input tax arises only when you receive the invoice, right?  Not when you receive a downpayment.

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