When not using Core Data, the only way to preserve user data is to store your database in the user Documents directory as well as the Library directory.
Documents
NSArray *paths = NSSearchPathForDirectoriesInDomains(NSDocumentDirectory, NSUserDomainMask, YES);
NSString *documentsDirectory = [paths objectAtIndex:0];
NSString *path = [documentsDirectory stringByAppendingPathComponent:[NSString stringWithFormat:@"UserData.sqlite"]];
Library
[NSSearchPathForDirectoriesInDomains(NSLibraryDirectory, NSUserDomainMask, YES) objectAtIndex:0];
These are also the only directories write-accessible to your app. If you have include a "blank" database in your Resources folder, it is copied to the bundle. From there, you need to check whether the db exists in the Documents directory, if not, then copy it from the bundle.
This is the only way to ensure that data is protected on app upgrades.
On another note, if the user does not backup their device, uninstalls the app then reinstalls the app, the data will be gone.
In regards to the user not being notified they will lose their data, the only thing that will prompt the user about loss of data is when they decide to remove the app from the device, or if you implement some way to notify the user of any data change.
If you would have set the version number to your database for your iphone could have been easily handle, save your version number into your db and whenever database is called, compare the version against the expected version
If new version > older version
change the schema (this is needed if you would have changed the schema of your database) with using SQL ALTER statements and update the app version number.
So whenever user is going to update or fresh installation, it will check the new version with your older version, if it differ then update schema, and if its same no need to make any changes.
If you would not have made any schema related changes (for example adding new column..) then you do not need to worry, user will not lose the data.
Source:- http://stackoverflow.com/questions/8459216/app-data-loss-on-version-upgrade