The .bak indices are populated from the data of the previous successful crawl, and serve as a backup of your last production index before overwriting it with the latest crawl. Therefore it is not unusual for the 2 indices to not be identical.
For more information about indices created by the crawler follow this link to our documentation: https://www.algolia.com/doc/tools/crawler/getting-started/concepts#indices-created-by-the-crawler