To move a set of site from one server to another one, start to make a backup like explain in the FAQ
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-268
Or with the help of the "weekly backup shell script" that you can modify to perform a backup of all sites in 1 shot.
www.jms2win.com/en/component/docman/doc_...weekly-backup-script
Once you have restored the backup on the other server, for simplicity, it is recommended to keep the same directory structure for symbolic links.
In the case where you restore the website on another directory, when you have restored the wesbites, login in the master and with the JMS "maintenance" menu there is the possibility to remove all the symbolic links and rebuild them.
Do it to reflect the new location of your master.
If you have restored the DB with different name, you will have to drop all the shared tables and rebuild them with JMS once you will have updated the DB name, login and password.
Convert the slave site into independent joomla is also possible.
The simpliest method consists in the install of JMS into each slave site site. (You can use the JMS tool menu)
After that, you have to perform a backup from SSH with command
tar -cvhz tarName.tgz slaveDirectoryToBackup
This command will perform a backup that will convert each symbolic link into a physical file and folders.
When done, you can restore the website.
Rename or remove the "multisites" directory to make it unavailable.
Make a copy of the "configuration.php"
After that, you will be able to uninstall JMS.
This will also restore the configuration.php from the master.
This will remove all the patches present in Joomla.
To remove the patches, you can also unzip an original joomla over the current one.
Restore the slave configuration.php
If you have sharing in DB, you will have to convert all the sharing into a physical copy.
There is no magic method. You will have to replace the views by physical content and also rebuild the table.