A web search finds several articles with sample code showing how to clear stray icons left in the Windows tray notification area when the application is killed (eg. by Task Manager or an updater application). For example this CodeProject example or this blog post.
Both examples above use a similar technique and are reported to work on Windows XP, 7, 8.1 and 10.
But how to get them working on Windows CE using the .NET Compact Framework? One problem is that FindWindowEx is required...but is not available in coredll.dll.