Are you certain the invoice posted?  You could try reprinting the invoice (to screen) and when you close the screen it should ask you if you want the invoice to be marked as printed....tell it NO.  Then you can try going back in to release the order again to create a new invoice and you will get a new chance to apply the deposit in the correct amount.  Of course, this will only work if the invoice isn't actually posted to their account which is what it sounds like since you are getting the unposted invoice message.  It may not work, but it could be worth a try.