Turns out the problem was not with the app bundle. Certain resources were being saved to the Documents folder (because newer versions were downloaded through the app) and the file path was being saved to the User Defaults. When the app was updated with a new version the file path becomes invalid because the newly updated app has a different uid in the path, therefore the resources stored in the Documents folder were not found.
I modified the code to always grab the file path from NSDocumentsDirectory instead of storing and grabbing it from User Defaults; I'm not sure why it was originally implemented to store the file path.