If vCenter was in linked mode running version 4.1 and you upgrade to version 5, when you try to join linked mode again you may find that you receive an error along the lines of Operation “Join instance VMwareVCMSDS” failed: : Action: Prepare for Join
1.From a command prompt with administrator-level privileges, change directories to the vCenter Server installation directory. 2.Delete the VMwareVCMSDS directory. 3.Recover the local LDAP instance by typing jointool.bat recover.
If all is well you should see the VMwareVCMSDS has been repopulated by running “jointool.bat recover”
Now try and run the join linked mode vCenter operation again, hopefully this time it will work.
Help with VMwareVCMSDS from http://www.vmware.com/support/vsphere4/doc/vsp_esxi40_vc40_rel_notes.html