For a phone app, it is separate from their browser app cache. They would need to go into settings, app setting, your app name, delete cache, and confirm.
I was testing one of my game awhile back ()
and it seems like the local storage data reset as I replace the app with a new version (it's not on app store, i'm just dragging it to my itune in this case).
And what was even weirder is that if I port using Cocoon.io. The local storage data reset whenever I close the app and reopen again. It was fine with Intel XDK which went out of commission from what I understand. I'm not too sure what to use at the moment too since I was off the book for a little bit now.