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When you go through the programming process, you Query the ECU to pull the ECUtek parameters -- including the license. I flash without an Internet connection. I do, however, update ECUtek software when I get a new tune. Just to ensure that the versions match up.
A partial flash will certainly bork things up. I made sure to disable and power saving features in Windows to ensure that it didn't put the computer or USB to sleep while programming.
Hope you get it sorted out!
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