I have inherited an application that uses an App_Themes folder. We don't support users changing themes on the fly. An admin changes the theme by editing the pages styleSheetTheme attribute in web.config.
I played around with configuring the Bundle.config with the following:
and then some includes like this:
<include path="~/App_Themes/Default/Default.css" />
Figuring that if an admin wanted to change the theme they could edit the includes to point to a different them without changing the styleBundle path which is used in the ASPX pages like this:
<%: Styles.Render("~/App_Themes/css") %>
However this doesn't work because the images referenced in the CSS in the theme aren't picked up.