Hi,
According to this kb :VMware KB: Upgrading to vCenter Server 5.5 best practices
"Before you upgrade any vCenter Server that belongs to a Linked Mode group, remove it from the Linked Mode group. Upgrading vCenter Servers that are members of a Linked Mode group can cause the upgrade to fail, and can leave vCenter Servers in an unusable state. After you upgrade all members of a Linked Mode group to version 5.5, you can rejoin them."
Hope it helps,
Regards,
Julien.