When a project has been marked as 'Completed', it no longer appears in the Payments screen. To apply a payment to a completed project, you can choose to create a new payment and select only the client when searching for invoices by client and project. This exposes all the open invoices for that client, regardless of the project status. You can then apply the payment to it. You can also select the particular invoice number.
Alternatively, you can change the status of the project to Hold or something else till all the payments are recorded for it.