Payment Entry Reference Issue

I have created two hundred supplier invoices and 50 debit notes (journal entry) for one supplier.

Now I want to make the payment to supplier against these invoices and using these debit notes.

Total Invoice amount - 100000
Debit Note - 5000

Payment = 95000

However, the payment entry reference child table is not allowing journal entry with debit balance while making supplier payment.

Its throwing one exception
Against Journal Entry {0} does not have any unmatched {1} entry.

Can someone please help?

Please use the payment reconciliation tool to reconcile the debit note against the invoices.

Practically it is not possible to reconcile more than 200 suppliers and with thousands of invoices and that is why I am using payment with reference.