While evaluating Visual Studio 2010 Beta 2, I see that in the converted directory, my vcproj files became vcxproj files. There are also
I just found that if you use Git you can mark .filter files to be treated as a union for merging to make it simpler. Just add the line:
*.vcxproj.filters merge=union
to your .gitattributes file.
See Using .gitattributes to avoid merge conflicts for more details.