Latest version of RBX [
http://hostingcontroller.com/english/downloads/rebuildXpress.exe ] does support backup/restore Shared SSL enabled sites on new machine. First you have to install Shared SSL certificate on new machine then you can run RBX restore setup to restore Shared SSL enabled sites.
Actually RBX creates SystemAccounts.csv file on backup which is readable to a thrid party tool ideal migration which can restore existing passwords on new machine.
On the other side RBX has the ability to reset the passwords and inform users about this new password by mail. You can check this option "Send new password notification each user" at the time of restore. This option is available under Rebuild Options tab of rebuildXpress.exe.