VS2010 ClickOnce File Associations

Revision 2
I have a Windows Forms App that was built with VS 2005 and uses ClickOnce to deploy. I am trying to update it to VS 2010. I wanted to upgrade to VS 2010 to take advantage of the fancier ClickOnce ability to setup proper File Associations. I made a test project in VS 2010 and found that the file associations worked like a charm. However, with my App, I am running into an issue. My old app contained code that manually added some registrty settings to get the file associations to work (at least on XP...couldn't get it to work properly on Vista and Windows 7 because of security/permission issues, which is why having the ClickOnce handle it is going to be so nice...). So now I have my upgrade app but the file association isn't working. I assume it is because that file association extension already exists for my old app. I assume this because when I click on those documents, the OLD program launches and opens the file. If I try publishing my upgraded app requesting a different extension for my file association it works fine. The problem is that I don't really want to use a different file extension because my users have many documents already saved with the old extension. Does anyone know a way to handle this situation gracefully?