Hi Gabrie,
You are right, when you deploy a new vApp from catalog, if a datastore is almost full then it will create shadow VM on another available datastore and create linked clone out of it.
I believe the same thing will not work for consolidation process, again I can confirm this behavior by tomorrow.
In meantime you may follow below steps to resolve the issue in present scenario.
- Storage vMotion the particular VM using REST API.
- This step will create shadow VM on the new datastore and migrate the VM to new datastore.
http://www.virtuallyghetto.com/2012/02/performing-storage-vmotion-in-vcloud.html
http://www.virtuallyghetto.com/2012/02/performing-storage-vmotion-in-vcloud_19.html
- Consolidate the VM.
Reference: