I may have found my issue, but this is subject to the next upgrade event.
When I right click the icon and go to its properties:
I see:
Notice the versioning info -- I think this is the issue. I originally pinned this guy to my taskbar by searching for it in the start menu, right clicking on the evernote icon that it found, and pinning to the taskbar.
However, if I navigate directly to C:\Program Files (x86)\Evernote\Evernote\ , right click Evernote.exe, and pin to taskbar, then clicking on the icon and looking at the properties does not seem to have version info:
Maybe this is the issue. Next time, Windows may not nuke the pinned item because it no longer has any version number associated with the link.