This issue can occur when customers are merged together in NetSuite. If you are merging customers in NetSuite, you should try to merge the newest record into the oldest one so the oldest record remains.
If you see an order in your error queue for 'Missing NetSuite Customer', select the order by clicking on the checkbox on the far left of the order.
and re-sync the order into NetSuite by clicking the 'Update Selected Orders to NetSuite' button.
The order should sync into NetSuite and auto-correct itself.