If you get a message that reads something link 'Parent X not found for job site Y. Please unlink customer in ServiceBox to relink or reimport the customer', this means that the link created between ServiceBox and QuickBooks for the job site's parent customer (note not the jobsite itself but the customer to which the job site is attached) has been corrupted in some way.
If this happens, simply unlink the customer in ServiceBox from QuickBooks Desktop and re-run the sync. This will either ask to re-link the customer (if the display names between ServiceBox and QuickBooks Desktop match exactly) or will ask to create a new customer. Once that is done the jobsite should come across during the sync.