Tilde (~), path, and deployment

I have been developing a web application in ASP.NET on my local machine using VWD 2008 and using the built-in "mini-IIS" feature. While developing I had everything saved in a folder called NIPR2. Here's the structure:
 

/ NIPR2

     - default.aspx

     - MasterPage.master

     / imagesFolder

         - image.jpg

 
All path references in my application use the ~ format. For instance, in the default.aspx there is a reference to MasterPageFile="~/MasterPage.master" and it works beautifully on my local machine.
 
On the production server I'm putting the directory in

/ wwwroot                       <-- "~" now points here

     / anotherApplication

         - default.aspx

         - someotherpage.aspx    

     / NIPR2                     <-- rather than here

         - default. ...
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