Bad idea.
This is not what "app.config" is designed for. Only the user is supposed to modify the file (which actually takes the name after the build: "youApplicationName.exe.config"). The idea is: you put some data you need to have by default to app.config. On build the file "youApplicationName.exe.config" is created and can be deployed with the application. (Normally, your application should work correctly even if this file is absent.)
The user can have this file and use it as a starting point and edit to change some configuration detail. The application is not supposed to modify it.
If, by some reason, you really want some file with some options modifiable by the application (not matter in what phase of the runtime), you can use a setting file. I would prefer some custom XML file built by
Data Contract which will directly serialize/deserialize some data classes representing some options/configuration. This file should be written to one of the locations known as "special folders" defined per user account of for "all users". For detail, please see my past answer:
How to find my programs directory[
^].
See also:
http://msdn.microsoft.com/en-us/library/ms733127.aspx[
^].
—SA