I can only think of two scenarios for this, seastoneconcrete.
If the invoice created was already paid, you'll have to manually update and mark it as paid. Here's how to record a payment.
Click + New.
Select Receive Payment.
Select the name of the customer from the drop-down menu.
From the Outstanding Transactions section, select the transactions that you’d like for QuickBooks Online to calculate. As you select these items, the payment total will change.
Select the payment method.
Enter Reference no. and Memo if applicable.
You can either deposit the money to your transaction account or to the Undeposited funds' account.