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Yes, it simply isn't designed to work that way. During testing, if you need to change the settings, do it on the fly to the *.exe.config file before launching the app and running your tests. Or do...

Ok. I believe there is a basic misunderstanding for what the app.config file is used for. It's for read-only settings that are read during program startup.

If you need some other functionality...

The simplest way is to change the app.config file located in the project's directory. If you make changes to this file, it will get copied over and renamed to myproject.exe.config.