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My plan is to delete the old Core Data stack (the NSManagedObjectModel .momd file & the NSPersistentStore .sqlite file) because:

In this case, is complete deletion the best way to go about migration?

It is a perfectly valid thing to do if your app requires internet access anyway. Otherwise users may be left with an empty data set (you delete the old database when you find it's incompatible with the current model, but you cannot re-populate it without access to the server).

Technically, that's a trivial thing to do. When you set up the NSPersistentStoreCoordinator :

NSURL *storeURL = ...;
NSManagedObjectModel *managedObjectModel = ...;
NSError *error = nil;
_persistentStoreCoordinator = [[NSPersistentStoreCoordinator alloc] initWithManagedObjectModel: managedObjectModel];
// Check if we already have a persistent store
if ( [[NSFileManager defaultManager] fileExistsAtPath: [storeURL path]] ) {
    NSDictionary *existingPersistentStoreMetadata = [NSPersistentStoreCoordinator metadataForPersistentStoreOfType: NSSQLiteStoreType URL: storeURL error: &error];
    if ( !existingPersistentStoreMetadata ) {
        // Something *really* bad has happened to the persistent store
        [NSException raise: NSInternalInconsistencyException format: @"Failed to read metadata for persistent store %@: %@", storeURL, error];
    if ( ![managedObjectModel isConfiguration: nil compatibleWithStoreMetadata: existingPersistentStoreMetadata] ) {
        if ( ![[NSFileManager defaultManager] removeItemAtURL: storeURL error: &error] )
            NSLog(@"*** Could not delete persistent store, %@", error);
    } // else the existing persistent store is compatible with the current model - nice!
} // else no database file yet
[_persistentStoreCoordinator addPersistentStoreWithType: NSSQLiteStoreType 
                                          configuration: nil 
                                                    URL: storeURL 
                                                options: nil 
                                                  error: &error];
                am getting this error SQLite error code:11, 'database disk image is malformed' at the initial launch after the update. But on subsequent launches, its not a problem as the sqlite files is deleted. But it seems i cant avoid this onetime app crash. And to feel that the app crashes immediately after the update is kind of disappointing. any ideas ??
– raw3d
                Jan 31, 2014 at 10:52
If you create a blank Core Data application you find the necessary code in Apples comments in the Application Delegate:
  
If you encounter schema incompatibility errors during development, you
  can reduce their frequency by:
  
Simply deleting the existing store: [[NSFileManager defaultManager] removeItemAtURL:storeURL error:nil]
  
Performing automatic lightweight migration by passing the following dictionary as the options
  parameter:@{NSMigratePersistentStoresAutomaticallyOption:@YES,
  NSInferMappingModelAutomaticallyOption:@YES}
        Lightweight migration will only work for a limited set of schema changes; consult "Core Data Model Versioning and Data Migration
  Programming Guide" for details.
        
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