Hi Jaime,
I am not surprised that you have the issue and there is nothing that can be done really. Hence the methodology for migration I suggested.
Justin Cooperman, is there something you can do ?
-Greg
What is the underlying issue here? It's not clear from this thread.
Were your template's containers and modules structured one way for a while and then you changed it to use a different structure?
If so, I wouldn't recommend completely overhauling the container structure or module structure on an approved template. You should do some upfront development and pick the element type for your containers and modules that works for your needs, then use them consistently from that point forward.
Still interested in what is happening and what the repro steps are. Please file a ticket.
Justin