If you have define a website that share content and that later you would like to have a physical copy, this is possible when you change the rule used slave site and remove all the sharing.
When done, you will have to use a PHPMyAdmin and drop ALL the views used by the slave site after that return in JMS to re-open/save the slave site definition to perform the copy instead of the sharing.
We strongly recommend that you perform a backup before dropping views.
Also ensure that you no more use any sharing anywhere in the website.
Also verify that the website that you are using to rebuild the physical data is effectivelly the website where the data is stored. If you are using a website that contain sharing that you want to replicate, the sharing will continue to be replicated.
If you want that we do that for you, this is possible with our billable support that you can order at
www.jms2win.com/en/joomla-multisite?page...35&category_id=1
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