Unable to completely uninstall standalone app called Etcher from Ubuntu [duplicate]
If you click "yes" to that message, a file called appimagekit-Etcher.desktop (or similar) is created in the following location:
/home/<username>/.local/share/applications/
To completely remove Etcher you have to remove the etcher .AppImage file as you described, and you should also remove this .desktop file. To do this, run the command:
rm /home/<username>/.local/share/applications/appimagekit-Etcher.desktop
replacing with the actual name of your home directory. Optionally, you can remove only this file if you just want to see the message again.