Question: Amazon didn't receive all of the units my supplier or I sent. How do I rectify that situation? Will Amazon, my supplier, or the shipping company reimburse me for missing inventory?
Step 1: When looking at your Manage FBA Shipments tab in seller central, you might see a discrepancy between what you shipped and what Amazon received (image below). Usually, Amazon will reimburse you for lost inventory.

Step 2: To "reconcile" these shipments and have Amazon reimburses you, you can request Amazon reconcile the shipment by clicking on the shipment and then clicking on the "Reconcile" tab (image below). Note that you can only reconcile a shipment once it's status is marked "CLOSED".

Step 3: In the Reconcile tab, you can select "Missing- Please Research from the drop down (image below).

Step 4: Then attach the requested document (usually just an invoice for SPD shipments and an invoice plus your BOL for LTL shipments).
In the additional info box, write: "Missing XX units of ASIN: XXXXXXX. Please research"
Within a few days, Amazon will usually reimburse you for the missing inventory. Amazon will usually reimburses you as if your sold the product (ie: Buy Box Price - Fees) so if you would have sold the units at a profit you will still make a profit!