Hello there, Jon.

Thank you for reaching out. If your QuickBooks account displays certain invoices as Unpaid despite having received payments, it's possible the payments weren't properly linked to their corresponding invoices.

To resolve this, let's start by verifying where the payments were recorded. You can follow these steps:

1. Go the the Get paid page and select Invoices.
2. Review the Invoice Details for each transaction:
   • Invoice Status
   • Invoice Amount
   • Linked Payments (if shown)

If payments are missing, let's proceed to record them manually or link existing payments by following the next step. 

Here's how you can manually record your payments to an invoice:

1. Locate the unpaid invoice under the Invoices tab.
2. In the Action column, click the Record Payment.
3. From the Deposited To dropdown, select the account where the payments was received.
4. Enter the Payment Amount and Payment Date.
5. Once you've completed these field, click Save.

If your customers made payments in cash, you can refer to this article for additional information: Record Invoice Payments in QuickBooks.

Feel free to reply to this post if you need further assistance.