If you get a message indicating that the invoice could not be found for a specific customer but that an invoice exists with the same number under a different customer, this is usually caused by an invoice being moved from one customer to another in Sage. This causes the link to disconnect between ServiceBox and Sage so it cannot apply payments.
The quickest way to fix this would be to move the invoice back to the original customer in Sage, then resync.
Alternatively, you could try moving the work order in ServiceBox to the customer with the same name as in Sage. This would move the invoice over to that customer as well and it may re-establish the link with Sage.