If you are changing the list programmatically why do you believe that it should be permanent? If it's permanent, why are you changing it programmatically? Doesn't make a whole lot of sense.
If you're talking about saving the values as "default" in the same way you do with the development environment, you cannot do this with an EXE. This is a FAQ. You have to update the list programmatically, saving the "new" default values to file.