Ionic Deploy and Cordova

I am trying to use ionic deploy in a new app, but I am running into a big issue.

Whenever I load the app I check for an update, and if so download and install (Using the manual method.) The problem is that after the app is loaded from the new local files, cordova.js is never loaded (I am guessing because of the new document root?) so all the plugins are broken.

Has anyone ran into this issue? Am I doing something wrong here? The app runs fine as long as I don’t call $ionicDeploy.load()