Applying Portion of Reconciled Deposit to an Open Invoice

Yes, we have the option to link the reconciled deposit to your customer's payment, ADVOCATES.

Here's how:

1. Find the deposit in the register.
2. Double-click the DEP line.
3. Delete the deposit line by pressing Ctrl+Delete on your keyboard.
4. Select the Payments button on the top.
5. Put a checkmark next to the payments that this deposit belongs to.
6. Once done, choose Save and Close.

For more details, please see this article: Correct Customer Payments That Have Been Deposited or Reconciled.

Additionally, I'd suggest running a Previous Reconciliation report in QuickBooks Desktop. This gives you details that can help you find discrepancies and other issues.

Please keep us posted on your progress in applying the deposit to the invoice. It's our priority to ensure your books are accurate.

The order is not quite right. You will have to Save the deposit without the payment in order to modify the payment.  You WILL get a popup about previous reconciliations and the way to avoid that (although you can always recheck the final saved deposit with the ;payment back in) is to enter a dummy amount from equity or any other holding account equal to the payment you are temporarily removing from the deposit.  Saving it with the exact same total should have no effect on the reconciliation as recon is only concerned with totals, not details.  

Once you modify the payment and add it back to the deposit delete the holding amount and Save.