The default keystore configuration protects the keys by using two levels of passwords - a keystore password and a password for each key. Currently, the keystore contains only a metadata secret key that is used for encrypting and decrypting node properties that are of type d:encrypted.
You can also configure a backup keystore. This is useful in case the keys need to be changed. The user can back up the main keystore to the backup keystore location and create a new keystore in its place.
If both the main and backup keystores are configured, the repository encryption works in the fallback mode. In this mode, the node properties are decrypted with the main keystore's metadata key first. If that fails, the backup keystore's metadata key is tried. The repository needs to be stopped and restarted for keystore changes to be picked up.
Keystores are used also to protect repository/Solr communications using encryption and mutual authentication. In this case, the keystores store RSA keys and certificates. For more information, see Solr 4 security.