I understand the concern over this payment not depositing after 3 business days. I am curious to know if the payment was by credit card or ACH bank transfer. The reason I ask is, depending on the pay method and your account's setup for deposit speed, there can be a 1-5 business day funding time on payments.
If you are not sure what your deposit speed is set to, please contact support and they can give that information. This link will take you to the QuickBooks support page, where you can select your service and the proper contact channel: Contact Support