VCloud does some ... well tricks... to work the way it does with Fast Provision. vCenter does not fully understand it. If you are using vCloud you really need to be careful and not perform actions in vCenter as this can cause issues with the vCloud based content.
(Now if nothing is linked from this base, I would assume the consolidate will work without issue, (but I think the doing operation from vCenter officially would leave the item in an unsupported state), but no need to perform this operation as it will just be undone next time the template is used).