I just saw your question at the end of your reply asking what account I was logging in with. I was using my privileged domain account, but the administrator@vsphere.local. I logged out and back in using the admin account and now I see all the vCLS.
I am not sure why this is happening. We recently changed our vCenters' authentication from Integrated Active Directory (because it kept creating RC4 cipher Kerberos connections to our domain controllers and InfoSec did not like that) to Active Directory over LDAP.
Our admin team security role still has global admin rights on the vCenter, but now we can't see the vCLS folder or VMs. I wonder what else changed.
This is very strange.