If you are using the downpayment functionality in ECC 6.0, you can do the following:
1) Mention advance against PO line item, create downpayment request and pay the downpayment to the vendor.
2) When capturing the invoice against the PO line item in MIRO, clear only the recoverable amount in the downpayment clearing tab.
3) The remaining advance will remain as a debit balance in the vendor special G/L.
However, just for my information, why is the advance non-recoverable?