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Kindly advice in Points in order we all can follow it and apply as well.
1) Make sure all invoices & Returns & Payments & Debits & Credits or any deductions before go through reconcile SOA.
2) Ask Supplier to submit updated SOA as of reconcile date i mean you both make cut off date to reach up for accurate balances.
3) Then classify the reconciliations into2 sections AS BELOW :
First : Transactions at Suppliers and not Yours ( Regardless its type ).
Second : Transactions at yours and not showed in Suppliers SOA.
But make sure all the above with the official supported documents.