The VIN of the bike is burned into the ECM of each bike, and the SERT is married to that specific VIN when its first initialized.
The Super Tuner is married to the ECM on the bike its originally mated to. It cannot be reused on another bike.
As an alternative if the situation isn't remedied by the dealer, there's an option of having the dealer reflash the ECM to the stock factory map and adding a TFI which would be a quarter of the cost of buying a new tuner with labor and dyno tune. It's an easy installation and you could do it yourself. Dobeck is here on the forum for any help you may need. I would go this route if they aren't going to help you out. The dealers love to sell the tuners because the profit margin is real healthy not only for the tuner but the dyno time added to that PLUS the extras that are necessary to use the tuner they sell. The tuner on the bike has to stay with that bike and can't be removed and reused on another bike, once it's married to the bike, it can't be reused.
Plus if it's the old SERT (the one that was made by TTS) Then you can mail the turner to TTS Smartune and they will reflash it with their new map (for the newer non HD affiliated) TTS tuner, for $100. Least it was that price a year ago. I garauntee that will be a better flash than the dealer.
The newer Screaming Eagle Tuners (forgot what year, 08 and above ?) are not made by TTS.
Lots of options here to choose from. If it were me I would have them flash the ECM back to the stock map at their expense to satisfy the customer. They made a profit on the sale and this is the least they can do if they want to keep you as a customer.There is no expense involved for the dealer other than the time the tech spends to do it.
Just don't fall for purchasing the new tuner from them with dyno time.