The concept of Jms Multisite is not based on synchronization that suppose that you duplicated the data.
The concept of Jms multisites is based on the sharing. So there is no duplicated data.
The sharing of the users is something decided when you create the website because you need ot have the same user ID for all the websites.
If you want to share the users after that the websites are already created, you must ensure that all the records have the same information before deleting the tables for the users and replacing them by a link.
As you will delete mysql table to replace by a link, you must ensure that all the records that will be deleted from the mysql tables are present in the future link.
In your case, the problem is more complex as you can not create a JMS template rule that will copy the slave site to build the master.
The only solution would be to do it manually or replace the master "users" table and all the permission by the one present in the slave site and later share the users that will be present in the master to replace the one in the slave site.
If you want that help you doing such thing manually, this is possible with our billable support that you can order at
www.jms2win.com/en/joomla-multisite?page...35&category_id=1