I have to put my truck back to stock from the 40hp setting to take it to the stealer. When I get it back and put it back on the 40hp setting does my truck have to go through the learning process again for the tranny?

mine did

the Allison is adaptive so any change in power it will have to learn again and adapt to the changes.

what briano says is true. however in my experience, take it how you will, the tranny learns a lot faster the second, third, and so on, time through. just my 2 cents.