Although there are a lot of posts about .net config files, I believe that my requirements do not allow for any of the solutions proposed (or I don\'t understand the process
Since you app.config file is a simple xml file you can load it into an XDocument:
string path = AppDomain.CurrentDomain.SetupInformation.ConfigurationFile;
XDocument doc = XDocument.Load(path);
//Do your modifications to section x
doc.Save(path);
ConfigurationManager.RefreshSection("x");
I corrected the XDocument.Load() code according to @Pat's comment