There is no 'solution'. Create a case and be like ... I just wanted to update you. We had a change in carrier and now this shipment # blah is shipping via FedEx with tracking blah, blah, blah.

You'll probably get a response similar to 'we can't do anything about it'. But this way you're ahead of the game and told them of the change in carrier while it's in transit. No need to explain what went wrong, just tell them there's a change in carrier.