Hi Ramcharan,
if you invoice product receipt - but you update on quantity field while you are doing the invoice, you will not be able to invoice the remaining quantity.
you have 2 ways to do this.
First one:
Add Misc Charges to vendor invoice in order to affect the product cost and then create a J.V in GL to clear the balance in Misc charges code and affect the vendor account, so the entery in GL will be
Dr. Misc. Charges Account
Cr. Vendor Balance
Second way:
is to create a debit not for the vendor "Purchase Order with negative quantity" and then create another for the correct transaction entry as MATTGUO says.