Why are my open invoices disappearing and showing as paid without being paid?

You're on the right track for your concern, @kylejarnott.

Let me share information about invoices in QuickBooks Online (QBO). When an invoice has been matched with a payment, this will be marked paid and closed. Since you're certain this has not been paid, we can double-check the transaction to verify and resolve it.

The available credit could also be a factor in why these invoices are marked as paid. You may have turned on the feature where the credit will automatically apply to open sales transactions with the specific customer.

Let's start verifying this one by following the steps below:

1. From the left navigation pane, select the Sales menu.
2. Go to the Invoices tab and look for the transaction marked as paid.
3. Tap the transaction to open the transaction summary window.
4. From there, you'll see the payment information linked to it.

You can press the Edit button to modify the transaction and unlink the payment if you substantiate that the payment is not intended for that invoice.

Once on the Invoice window, click the payment link under the Payment Status. Then, hit the Dates. You will be routed to the Receive Payment window. From there, scroll down to the bottom and press Clear Payment. To save the amendments, please click the Save and close button.

Furthermore, you can refer to this article to categorize your payments and other transactions. They will aid you with putting them into the correct accounts. Afterward, reconcile your account to ensure this is balanced.

If you have more concerns about invoices, you can always post them here for assistance. Have a good one!