This may be the simple question to answer, but I am struggling to resolve.
I have Web.config with the following values in my Web Application.
While I don't work often with web applications, in my desktop application I often face a similar issue. I've been using the code provided by Daniel Hilgarth https://stackoverflow.com/a/6151688/2212458 to temporarily switch configuration files. The plugin loader can pull in the plugin configuration file and then restore its own.