Hi julianatterton!  Yes, we can Delete a Customer Payment, then re-apply that to specific Invoices.  To do that just click on:

1.  Customers and click on the Customer

2.  Here you will see all the Payments and you can click on Payment, and down at the bottom of the Payment is More, then click on Delete (see pic 1).

3.  Now you can click on Create (+) and Receive Payment (see pic 2)

4.  Then enter your Customer's name, enter the Bank where it is being Deposited, Enter the Check Details and Amount and check off all Invoices you want the Payment to apply.

Please let me know if that helps, and thank you for being a QuickBooks Online Customer!