I appreciate you posting again in the Community, @Rita_89.

You have the option to link the reconciled deposit to your customers' payment. This way invoices will be marked as paid and will zero out the outstanding balance.

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 check-mark next to the payments that this deposit belongs to, then choose Save and Close.

You may also refer to this article for more information about handling reconciled payments and deposits: Correct customer payments that have been deposited or reconciled.

I want to know how this goes on your end. Hoping to hear from you again. Take care!