Yes, adding it programmatically is frowned upon but if I have manually pinned an application I expect it to stay pinned after upgrading. Great tip! I wish I didn't need to do this, but it is a good workaround. Note: You can create the shortcut anywhere, you don't need to clutter your desktop if you don't want to. I put my shortcut under "My Documents".
+1 I am not sure why the Windows taskbar keeps losing the pin setting, but it must be something Evernote is doing during upgrade. Other applications (Firefox and Chrome for instance) aren't affected when they are upgraded.