Not upgrading plugins is a really bad idea. I can't support anything other than the "current" version of a plugin, and there is nothing more frustrating than having time wasted on a bug that has already been fixed. Periodically calibre changes things internally which require plugins to be updated as well.
You won't lose any settings when you upgrade a plugin (or at least none of my plugins I can guarantee that with), just like upgrading calibre won't lose your books. So just do the upgrade and the message will disappear.