I wish it was that easy of a fix! I have a bad clunk—obnoxiously loud—when I come to a complete stop after going 35+ mph. Right when I hit the 10 mph mark, the clunk always happens. It feels like multiple gears are dropping at one time and you can feel/hear it.
I ordered a Cobb Accessport, so I was going to run a tune and see if when the adaptive tables are reset, the clunk goes away. But it has me concerned that something else could be wrong with the transmission because it is butter smooth everywhere else.
I had a friend that faced such a problem when he changed his old engine. The problem was related to the pcm and tcm connection.And all the necessary updates and flashes were done with no improvement the last thing I heard was the valve body was damaged and they asked for a ridiculous amount of cash to change it, and my friend went with a used trans and things are going well with him.
I hope its not the same case and you get it sorted out with a flash.