Since version 2.5, Moodle uses individually salted password.
In order that user accounts of two parallel Moodle sites may still be synchronised (including their passwords), it is necessary to add a new feature to the External Database authentication plugin so that Moodle can manage individually salted password of an external Moodle database.
A way to this would be to add a new Password Format to the External Database authentication plugin to deal with External Moodle Databases (a "Moodle password format"), see the external database configuration page admin/auth_config.php?auth=db
A Moodle site should be able to exchange user informations with another Moodle site, including their passwords, which is impossible for the moment.
See the discussion https://moodle.org/mod/forum/discuss.php?d=246474