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.
Update May 22, 2019
I case anyone else than me still does maintenance work in Compact Framework the commenters are absolutely right. The Power Toys for .NET Compact Framework 3.5 (https://www.microsoft.com/en-us/download/details.aspx?id=13442) is much easier to install than reinstalling Visual Studio.
But what I’ve done a few times is just copying the files named *CompactFramework* from another computer, that also has Visual Studio 2008 installed, into C:\Windows\Microsoft.NET\Framework\v3.5. Or just save the *CompactFramework* files in another folder or a network drive until the next Windows Update.