Hi. Sorry for the delay in getting back to you. As you explained, selecting prepayment posts the VAT into a VAT prepayment account and remaining to the vendor account. This conflicts with the input VAT that is charged at the customs / port in case of import since their VAT includes the shipment VAT, VAT for handling etc.
In our system, the PO does not include VAT as it is set to 0% for all foreign vendors and we are currently posting such import (input) VAT manually through GL for such cases. Any vendor VAT is part of the the total PO amount itself as it is not applicable in our country. So for prepayments, we came up with below options:
1) Use Prepayment option
In case of 100% advance payments, we can use the prepayment option with a VAT prepayment ledger account setup to hold the VAT. For foreign vendors where we make advance payments, the VAT is 0% (sales tax group FVAT). So in case of such prepayments, the VAT will be zero and the entire amount will go to the vendor itself and VAT will be posted manually after material receipt through GL as mentioned earlier.
2) Without using prepayment option
The payment via Accounts Payable is done without selecting the prepayment option (even if it is a prepayment). This is the then settled with the purchase invoice amount later. VAT isn't a concern here since it is posted manually as a journal between the Tax Authority and Input VAT. Tax Authority is paid directly from bank.
We are currently using the second option. We had to reverse a few AP payments to repost them without prepayment option selected.
Thanks again for your support Dr. Ludwig.