If you have move the master website location on the disk, you need to rebuild all the symbolic link on the disk to reflect the new location on the disk.
See the FAQ concerning the manual backup/restore procedure.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-268
In summary, you have to delete all the symbolic link and go in JMS "site manageer" to open and resave each slave site.
Check the content in the "/multisites/config_multisites.php"
Potentially delete the "master" cookies and master directory path.
Delete all the symbolic links present in each slaves sites "deployed directory".
Delete the "index.php" and "index2.php" present in the root of each "deployed directory".