[Gregski]

after you made your changes, and saved your new file with a new name, something like 01 - No VATS then you can click on the black chip with the red arrow icon on the menu to launch the Vehicle Writer

Keep in mind Reading is no big deal, but Writing is dangerous and can be destructive, now you aint gonna blow your engine up but you may brick your PCM, so don't be wiggling any cables or getting in and out of the vehicle, or playing with the radio, and if things freeze just be patient and wait, it may take some time.

Also if you are having difficulty writing you may want to try doing it with the Use High Speed check box unchecked.