Debit Note entry for rate discount - Stock valuation Issue

I purchased 1000 pcs items for sale @ 200/- per unit,with update Stock I have made the purchase invoice & the GL entry passed like this:
Stock A/C Dr 2,00,000
Creditor A/C Cr 2,00,000

Supplier issue a credit note for rate discount of Rs-6 per unit, now when I am making the debit note entry from purchase Invoice with unchecked updating stock filed the system passed the GL Entry like this-
Creditor A/C Dr 6000
Stock Received But Not Billed Cr 6000

Due to the above transaction the supplier ledger is adjusted though the stock value is not deducted and the closing balance of stock is also unchanged (Where actual stock value is (200000-6000)=196000.

How to resolve this type of issue, if anyone suggest the right procedure to handle this type of issue is very help full.

Thank You.