I"m not quite sure, but I recommend that you put your S3 settings in ENV variables as described at Configure an S3 compatible object storage provider for uploads. You’re likely to have trouble restoring a backup with the settings in the database.
Also, if you do have them in app.yml and have the backup on S3, then you need only the yml file to set up a new server and restore the database.
If it’s possible, sharing a topic where you have this problem will give someone trying to see what’s going on a lot more information. If your site is public, then the only thing you need to hide are your keys, which are already hidden.