We recently worked on a fix around Biztalk Project System for Biztalk 2009; to be released as KB 979096. The issue was about the project extension being remapped as CSProj instead of BTProj. The problem surfaced whenever a generated item/schema was added using the "Consume Adaptor Service" option.
The problem was around the way VS interpreted the project type. EnvDTE.Project.Save() understands btproj to be csproj internally, and when filename is provided, it appends .csproj to it. When no params are passed for filename, nothing is appended. The fix was to simply not pass the param 🙂
Instead of using EnvDTE.Save("ProjectName.btproj"), use EnvDTE.Save(string.Empty).
This fix should be avaiable soon.