When a deposit is included on an invoice and the parent has paid it, reconciling the invoice will add that deposit as income.
You can deduct the deposit from the Income section by following these steps;
From the Admin Dashboard, expand Administration and select Accounting
Click the Income tab and then Add new item
Enter the details as below and click Save.
The date should be the same as when you reconciled the original invoice
The amount should be entered as a negative
This will create a record of the deposit on your system and deduct the amount from your total income.