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If they program your car, they will bring ALL the car's firmwares to the latest software version. They have NO WAY to skip certain firmware upgrades (for example the transmission) while programming. My dealer took me to the programming department and showed me all the steps.
But luckily every programming generates a log with which modules needed programming. This is usually attached to the work order. You can ask this print from the dealer and you can check if the transmission module was programmed or not.
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