Vendor credits from Amazon for various transactions, such as FBA reimbursements, will have an a deposit associated with the credit. However, because the two transactions are not linked, the accounts payable will reflect the "missing" deposit.
In order to link the deposit to the vendor credit, you will need to create a Bill Payment in order to mark the credits as paid so that the accounts payable can be updated to the correct amount.
To create a Bill Payment, click on Expenses, then Vendors. Next, click on the gray "Open Bills" button. Find the Amazon vendor account and click on "Make Payment" link.
QuickBooks will bring up a Bill Payment window and automatically link the deposits to the vendor credits. Select the Amazon Undeposited Funds account.
The total balance should be $0.00. If it is, click Save to add the Bill Payment.
If the balance is not zero, you will need to review the selected transactions and only include the vendor credits and deposits for those credits.
Once saved, the A/P account will be updated with the correct balance.