That file has never existed at that location. It has always been clientscript/ckeditor/_source/plugins/plugin.js
VaultWiki doesn't reference the ckeditor files directly. It simply tells vBulletin internally to send the editor HTML, and all the Javascript for it is handled by vBulletin. Either there is a bug in 4.1.6, or you have another mod installed that references the file directly and uses the wrong path.