I’m having a similar problem with localStorage but when I uninstall/reinstall the app and then I open the app from the AppStore/TestFlight app It skips some validations that rely on localStorage being empty is like if the context of the localStorage is being persistent when doing app-linking navigation on iOS9 (Opening the app from the appStore also adds a backButton on my app).
This is just a guess, is hard to debug this corner case because the app in the store cannot be debugged.