We are experience the same issue you described, and I was wondering if you ended up finding a solution? I keep getting the "The following assets are in use or used by other assets:" error.
Just wanted to chime in here and say that Josh Hill's advice is what fixed our problem cloning across workspaces. All assets that had the error message were using templates in unshared folders. Once all the templates were shared we were able to clone successfully. Hope this helps!
In case you're still struggling with it in 2019, just to confirm Josh Hill's advice is still coreect and saved my time a lot!
Thanks all 🙂