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