I have an SQLite database in the first version of my iPhone application (which is on the app store). Now I want to roll out the second version of the application, which also
This isn't something I've personally tested, but to the best of my knowledge:
christo16 is right, and assuming that your already-shipped app didn't copy the db out to Documents, you might want to ship an interim version that does do this. Then it'd just be a matter of making sure a critical mass of users have installed the interim version before you roll out the db updates.