I found this post on the BizTalk Customer Response team blog about the problems people are having with the BizTalk project system integrated into Visual Studio 2008. Apparently, the team built very closely on the C# project type, but that integration is causing some problems as any patches to VS can cause values to be overwritten, removing the relationship of the btproj to the csproj projects. I have run into this on several machines and always had to repair the BizTalk installation in order to fix it. That takes more time than I think it should to fix this type of problem, so I was glad to see the solution is a simple registry edit.
You should be able to create a reg file the following contents to fix this on an x86 box:
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VisualStudio\9.0\Projects\{FAE04EC0-301F-11d3-BF4B-00C04F79EFBC}]
"PossibleProjectExtensions"="csproj;btproj"
For a 64-bit installation, you can use a similar file, but with a slightly different path for the key. So the reg file would look like this:
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\VisualStudio\9.0\Projects\{FAE04EC0-301F-11d3-BF4B-00C04F79EFBC}]
"PossibleProjectExtensions"="csproj;btproj"
I plan on having these registry files around on my machines with BizTalk developer tools on it so that I can quickly apply this fix anytime I patch (or Windows Update patches for me) my Visual Studio installation.