There are two ways:
1) Void the invoice.  This creates a credit memo, puts the inventory back, and reopens the sales order with the quantity returned on it.  
2) If you do not want the sales order to be re-created ( because they are not being shipped another of the same item) create a new sales order with a negative  quantity and a price per each equal to the original sales price.  Release the sales order and invoice it.  This puts the inventory back, creates a credit memo, and closes the sales order.
 
Hope this helps.

If the invoice for the shipment was $0 to the customer, you can just perform an inventory adjustment IN-C, type A, adding the shipment qty back to inventory, and enter the value, if any, at which you want the inventory to be carried.  
 
This method will not reopen the sales order.

I suggest voiding the invoice, zeroing the original quantity on the sales order then closing (and purging) the sales order.  I don't know where you live, but I would not suggest eliminating the invoice from the system ( not even sure you can!) without a paper trail--  I live in CA and have been through a sales tax audit......