I agree in getting the dealer to provide this no cost since you are still under warranty. Not only for that reason, you also had to install a new battery which should be under warranty.

 

Wow. That is probably the most ridiculous bs I have ever heard. I have disconnected my battery many times and recently replaced it and not once have I needed a reflash. Sounds like a dealer trying to make a buck off owner stupidity.

 

the pcm doesnt forget its programming from disconnecting the battery. it loses its adaptive strategy (keep alive memory). the pcm learns and adapts and that learning is reset when the pcm loses battery power or kam is cleared using a scan tool. the reflash is supposed to correct the trans shift issue caused by reseting kam. other issues are possible do to loss of battery power to the pcm, more common is idle issues for higher mileage vehicles with electronic throttle bodies that have some sludge build up.
your battery is also under the factory warranty, 3/36 gives you free replacement. you could try for reimubursment from ford. ask at the dealer when you go in and have your reciept from the battery purchase with you. if you continue to have problems with that specific dealer, call the 800 number for ford customer service. they will follow up with the dealer to resolve any concerns. its not just a complaint line, the dealer gets contacted when customer service interaction required.