You can delete the payment on the invoice you've marked as paid. Doing this will clear the invoice paid status. Let me walk you through how to delete an invoice payment.
Go to Sales or Get paid & pay in the left navigation menu.
Select the Invoices tab.
Find the invoice and open it.
On the upper right, click on Payment made hyperlink and select the date.
On the Receive Payment window, click on More and select Delete.