As a workaround for when you want deposits or overpayments to sync to your accounting software we follow the following procedure. This will then allow the payment to sync over to your accounting software so that the payment can be reconciled.
As you are reconciling this payment in your accounting program please do not void the invoice as this will undo the reconciliation in your accounting program,
1. Create an invoice for the deposit amount. You can create a product called deposit, then apply the amount.
OR if its an account customer apply the payment to the invoice. Once the invoice is processed it will then sync to your accounting software.
2.You will then need to create a Credit for that customers account. Which you will need to Void once the invoice has been processed
Here is how to create a credit: https://workshopsoftware.com/knowledge-base/customers/how-to-record-a-credit-or-deposit-against-a-customer/
You will need to make sure it is an account type credit to do this switch Account type toggle to ‘Account’.
3. Create an invoice for the customer of the work you have done for them. Once the Invoice is completed and saved (BUT NOT PROCESSED) add a discount to the invoice for the value of the deposit.
Then process the invoice
Here is the link apply discount: https://workshopsoftware.com/knowledge-base/job-centre-invoicing/apply-a-discount-to-a-customer-invoice/
4. After the customers invoice has been processed, Void the credit note you made to the customers account.