In QBO, go to the Sales menu at the left pane to get to the Customers page.
Click the customer's name to open the Transaction List.
Locate the payment and select it to open.
Tick the More option at the button and choose Delete.
Hit Yes to confirm. The customer will have an unapplied payment which you can either delete or apply to future invoice(s).
Once done, your client can now pay the invoice by having them click the Pay Now button. I'm also adding this article that tackles how to let customers pay their invoices online for future reference: Take and process payments in QuickBooks Online.
Please leave a comment below if you have any additional questions or concerns. I'll be more than happy to help. Have a great day!