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