After installing Update 10586.3 from Windows Update the Compact Framework projects could not be loaded in Visual Studio 2008. The error was something like “C:\Windows\Microsoft.NET\Framework\v3.5\Microsoft.CompactFramework.CSharp.targets’ cannot be found.”
I haven’t found any explanation of why this file (and some other Compact Framework files was removed during the update.
But the simple solution was to do a Repair/Reinstall of Visual Studio 2008.
Update August 17, 2016
Now Windows updated to Version 1607 (Build 14393.51) and the same problem is back again. It looks like we will have to do a reinstall of Visual Studio 2008 after each update of Windows 10.