When you write a check to a customer and use A/R as the account, QuickBooks thinks you just made a loan that should be repaid and this increases A/R.  If you had posted the original deposit to A/R, there would’ve been a negative balance equal to the amount of the refund so the refund would’ve brought the account back up to $0.

Assume the deposit was $1000 but you only did $800 in work.  Your transactions probably looked like this:

$1000 Deposit:
Increased cash $1000
Increased revenue $1000

$800 Invoice:
Increased revenue $800
Increased A/R $800

$200 Refund Check:
Increased A/R $200
Decreased cash $200

In the above scenario, both revenue and A/R are overstated by $1000.  Not only that, but this isn’t really the proper way to handle customer deposits because you’re booking $1000 in revenue before you’ve actually earned it and as you learned you sometimes have to refund some (or all) of the customer deposit.  This is how they should be booked:

1. Go to Lists > Chart of Accounts, click on the Account button, select New, and add a current liability account called "Customer Deposits".
2. Go to Lists > Item List, click on the Item button, select New, and add an other charge item called "Customer Deposits" mapped to the Customer Deposit account you setup above.
3. Create an invoice or sales receipt using the Customer Deposit item you created above, and receive payment as usual.
4. On the final invoice, invoice for the full amount of the contract and add a line using the Customer Deposit item using a negative amount for the deposit already received. The total on the invoice should show the remaining amount due.
5. Periodically go to Banking > Reconcile and reconcile the Customer Deposit account so that the customer deposits that have been applied to invoices are marked as cleared.
6. Then you can filter a report to only show uncleared transactions to get a report of only customer deposits that haven't been applied yet.

In this case, if you owe your customer a refund you’d use the customer deposit account which should still have a balance equal to the amount that should be refunded because it hasn’t been invoiced yet.

The transactions would look like this:

$1000 Deposit:
Increase cash $1000
Increase customer deposits $1000

$800 Invoice:
Increase revenue $800
Decrease customer deposits $800 (leaving a balance of $200)

$200 Refund Check:
Decrease customer deposits $200 (bringing the balance to $0)
Decrease cash $200