Look at it like you would a regular computer.
If it gets all messed up for some reason, then reloading the OS usually makes it better. But then, it's sometimes hard to get it back exactly the way you like it.
If it's running fine, don't try to fix it. Sometimes you just gotta know when to leave it alone.
In rocketjock's case, he just followed instructions. But now he is having a hard time getting it all back the way it was. Perhaps those instructions should have warned him.
Between my Ranger and my first Taurus, I've been through it 5 or 6 times due to dead battery or overseas shipping. A friend had told me if it ever happened, to be sure to drive exactly like I normally did for a few days. Some extra accelleration, or lack of it, can result in the computer learning something other than you want. Each time I had better luck than rocketjock.
My advice is not to reset the computer if the vehicle is running the way you like. If it seems all messed up, then reset it - but drive the truck like you want it to learn for a few days.