You posted this in the subforum for discussion about the forums themselves, not about programming topics, and you tagged this with both "ios" and "nsdocument", so it's not clear whether you mean iOS or OS X. I'm going to assume iOS. The answer may be the same for OS X but I have no experience there.
App updates on iOS don't touch any files in your app sandbox. The absolute path to the sandbox may change but the contents of individual directories (Documents, Application Support etc.) should not be touched. So when your app is launched for the first time after the update, it is up to you to detect that it's an update and do any migration of your app data if necessary.