In my experience, it's often unnecessary to create multiple project files to perform multi-targeting. Instead, we let MSBuild do the work for us.
msbuild MySolution.sln /ToolsVersion:2.0 /t:Rebuild /p:Configuration=Release
msbuild MySolution.sln /ToolsVersion:3.5 /t:Rebuild /p:Configuration=Release
msbuild MySolution.sln /ToolsVersion:4.0 /t:Rebuild /p:Configuration=Release
msbuild MySolution.sln /ToolsVersion:12.0 /t:Rebuild /p:Configuration=Release
The "12.0" isn't a typo. MSBuild used to be part of the .NET Framework. It now ships with Visual Studio. In VS2013, it's called MSBuild 12.0.