@ahmadmusair_3593, that is an excellent illustration and explanation. I can duplicate this problem and am moving the topic to the Bugs category.
@lubos, what happens is that Accounts receivable is properly credited by the credit note. But Inventory on hand and Inventory - cost are credited and debited respectively for zero amounts, even though there is a non-zero average cost for the inventory item at the moment the credit note is created. The transaction is posted to the two accounts, but at zero amounts. This occurs whether or not the credit note is specifically designated for a pre-start date sales invoice.
I can think of no reason the program should treat a credit note differently in this situation, just because there is a pre-start date sales invoice for the customer.
I also have not tested to see if the same problem occurs for debit notes, but I suspect it might, given their parallel structure.