The payment will sync for individual invoice payments.
For this scenario, you can mark each invoice as paid. Just enter a note saying the payment didn't sync to them You can also wait for the payment to be downloaded on your Banking page, and match them to your invoices.
You can always go back to this thread if you have some questions.
Hello there, Switch87,
You can also link a deposit to an invoice. When you receive bank deposits as a payment, you'll want to link them to the customer's open invoice.
Next, apply the deposit entry as an invoice payment.
Don't hesitate to reach out to me if you need more help.