What do you mean by "moved appropriately"? The problem you mentioned is with orphaned controls - those are controls whose parent does not exist in the page. This is why they are not shown. If you run the script, they should be moved to some correct placeholder and should be visible in the backend. If they are not, then they are probably not moved correctly.
In the service pack that will be released this week special handling is introduced in relation with orphaned controls. Those controls will not be visible in the frontend, but will be visible in the backend, where you will be able to place them in their correct placeholders.I suggest that you wait for the 4.1 SP1 release and try how things work there.
the Telerik team
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