I have looked here and here and almost found the answer to what I'm looking for but not quite.
If I publish a new version of my app and the user launches their install they will be prompted to install a new version. At which point, the entire App.config is overwritten with the published version. I would like to maintain the App.config between upgraded versions on the local machine install.
The links above don't solve my issue because I am not using the Properties.Settings.Default namespace but rather custom config sections in my App.config called with ConfigurationManager. Thus I need an exact copy maintained of my App.config between upgrades.
Thank you