If you have invoices that are paid in QuickBooks but they do not show as Paid in Pencil, the usual cause for this type of issue is that the QuickBooks integration has been disconnected from Pencil.
To resolve this, you can go to https://support.pencilpay.com/knowledge/how-to-connect-your-quickbooks-account-to-pencil you may need to disconnect QuickBooks first by toggling OFF the green switch in the top right and then reconnecting QuickBooks.
This may solve most of your issues that shows invoice as Paid in Pencil but not in QuickBooks and the same is true vice versa (Invoice shows Paid in QuickBooks but not in Pencil).
If you want to re-push the payment to QuickBooks, follow these steps: How do I re-push a payment from Pencil to my accounting software (pencilpay.com).