I am not familiar with how the Cortex tuner works - can the files be emailed like the Vector tuner? If so just get it from someone else.
If not, I'm SURE that another Texan would allow you to user your Cortex on their car once they return it to stock. copy their stock tune, then you can install that on your car. I had shifting issues with mine just after I got it and the dealer changed my tune as well. Luckily for me I had not yet ordered my tune so didn't run this risk.
Even if you had to drive a few hours to get to someone I think it would be worth it (as opposed to losing dealer support for the transmission)...
An final option would be to borrow someone's Vector PowerCal and one of us can send you the file you need if the owner doesn't already have it (you might have to buy the tune from them if borrowing violates their Rules of Use).