Only testing would confirm how the update process for your application works. Here is what the document says:
Files Saved During Application Updates
Updating an application replaces the
previous application with the new one
downloaded by the user. During this
process, iTunes installs the updated
application in a new application
directory. It then moves the user’s
data files from the old installation
over to the new application directory
before deleting the old installation.
Files in the following directories are
guaranteed to be preserved during the
update process:
- Application_Home>/Documents
- Application_Home>/Library/Preferences
Although files in other user
directories may also be moved over,
you should not rely on them being
present after an update.
Details here http://developer.apple.com/iphone/library/documentation/iPhone/Conceptual/iPhoneOSProgrammingGuide/RuntimeEnvironment/RuntimeEnvironment.html
The Feedback Service
If a provider attempts to deliver a push notification to an application, but the application no longer exists on the device, the device reports that fact to Apple Push Notification Service. This situation often happens when the user has uninstalled the application. If a device reports failed-delivery attempts for an application, APNs needs some way to inform the provider so that it can refrain from sending notifications to that device. Doing this reduces unnecessary message overhead and improves overall system performance.
For this purpose Apple Push Notification Service includes a feedback service that APNs continually updates with a per-application list of devices for which there were failed-delivery attempts. The devices are identified by device tokens encoded in binary format. Providers should periodically query the feedback service to get the list of device tokens for their applications, each of which is identified by its topic. Then, after verifying that the application hasn’t recently been re-registered on the identified devices, a provider should stop sending notifications to these devices.
http://developer.apple.com/iphone/library/documentation/NetworkingInternet/Conceptual/RemoteNotificationsPG/CommunicatingWIthAPS/CommunicatingWIthAPS.html#//apple_ref/doc/uid/TP40008194-CH101-SW1