I tried uninstall with App Cleaner, updated the OS, and reinstall, but happened again. So, I have no idea how bad this idea is, but I decided to remove this process manually. Since then, I've never seen the problem. Here is how to do that; Run Terminal Type this command and enter rm /Applications/Evernote.app/Contents/PlugIns/EvernoteSpotlight.appex/Contents/MacOS/EvernoteSpotlight Hope this helps you.
The pop-up displays "EvernoteSpotlight quit unexpectedly." repeatedly. So annoying. How can I stop this? It's ok Spotlight not targeting Evernote contents, just want to kill that message.