If you adjusted the qty/value of items not received to COGS shrinkage, then you are saying that you bought those items and now they are gone so that is why they are in the shrinkage account.
If that is the case then pay for them
But what really should have happened is that you enter a bill, and enter a qty of zero for those items not being provided. Entering a zero in the qty column results in those items not being included in the total for the bill.