Greg,
Glad to see some Lab Manager people around here 
The workflow with Lab Manager is surprisingly similar, but the details were hidden.
In Lab Manager, you would 'unpublish' a template. This process created a new child link in the chain to store changes. This is eqivilent to copying a vApp from Catalog to 'My Cloud' for editing purposes.
Once you did the update in Lab Manager you could then publish. The difference is with vCloud, that you have to make 1 more additional link in the chain to put it back into the Catalog.
However, the performance degredation as chain length increases has significantly reduced. If there is VAAI support for linked clone chains on your storage, e.g. Native Linked Clones, then it's even better from what I hear.
If you run this process and delete the original from Catalog, nothing will be damaged. The pre-existing VMs based on the "previous" linked clone chain will still exist. vCenter manages these linked clone chains now, as Shadow VMs.
Lab Manager just did all the micro-management in its Database and Datastores, as undeployed objects were not listed in vCenter invetory.
As always, if you want to consolidate VMs in the Catalog of vCloud ... that'll reset chain length and start a new Linked Clone tree for any VMs created from that vApp/VM afterwards.
I hope that helps.
Jon Hemming