When submitting an update to an app to the app store (via iTunes Connect?), is the update necessarily a whole binary? Can an update come in the form of a patch? If a second version of an app shares a lot of assets and logic from the previous version, does all that logic/resources get reinstalled wholly regardless?
There are no patches. It's installed as an entire read-only bundle. The old bundle is replaced with the new bundle.
Application data is retained (ie. documents folder, NSUserDefaults).