Path issue implementing an application inside an Asp.net Webforms Site

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http://serverfault.com – We have a web site running on IIS7.5 using Asp.net web forms. All the website paths are in the format: "~/". Inside this website we have an application that loads inside an iFrame tag one page of the parent website. Obviously all the reference paths in the iFrame content are referred (and point to) the application root and not at the website root. Is there a way to let point the iFrame content to the website root only changing the application or at least the website web.cofing, but not making mods on the website code? (HowTos)