It’s always a bad idea to delete internal files of a plugin, unless told to do so…
As said, I have published an update to LOTT, v2.0a, which makes the notification at startup more explicit, so that you can find out which extension icons is referenced in your palettes and is not installed in your environment.
Anyway, the LOTT notification is just an information. It is shown at startup and disappears after a few seconds.