How to close PO that was short shipped

Summary:

In Relation to a BPA. If a supplier is unable to deliver the full qty for the PO and it is outside the defined tolerance, How do you close the PO? How does the remaining amount go back to the BPA

Content (required):

If we have a BPA for S10,000

We release an order for 1000 widgets at $1 each

The supplier can only supply 600 widgets

What is the process for closing this PO when only 600 of 1000 have been delivered and this is outside the defined tolerance?

How does the $400 get added back onto the BPA? 

Version (include the version you are using, if applicable):