Ivan,
When I last traveled home from Walt Disney World and used the Resort Airline Check-In, it did have the most updated information in place for my flight home.
What they will have you do at the resort Luggage Desk when you are checking out is have you call a central phone number where, if you did have to pay for bag shipping, you could provide a credit card for billing. They should have the most up to date information, if your airline has provided it to them.
However, they cannot, to my knowledge, make the upgrade change itself, so if that is something you still need to do, you should contact your carrier directly.
Have you confirmed that your airline participates in the
Resort Airline Check-In program with Walt Disney World? Not all do. I have linked above to the page that lists them.
I hope that this helps? If you have any other questions, please send them along!
Have a magical vacation!