The `uplaods:migrate_to_s3` rake task should always use the environment variables, because you usually don't want to break your site's uploads during the migration. But restoring a backup should work with site settings as well as environment variables, otherwise you can't restore uploads to S3 from the web interface.
The rake task aborted the migration with "Already migrated" when all upload URLs linked to the correct S3 bucket even though the files didn't exist on S3. By removing the first check we force the rake task to check for the existance of uploads on S3.