Be sure that there is no confusion between Earnest Money Deposit and Good Faith Deposit. I have found that Realtors in different areas use different terms.
Good Faith Deposit is generally provided with the offer and in downstate (Long Island), we generally do not collect this.
A down payment is generally provided in two parts; an amount at contract signing and the remainder at closing, along with the mortgage.
The definition of a contract requires signatures of both parties and a value (money) or it does not constitute a contract.
I would be happy to refer you to some mortgage banker/brokers who could probably respond much better, but I do believe the down payment required to create a contract in your case will be refunded at closing.