Jamrock,
What you would probably have to worry about most is the shock to the roots, and root damage. Someone wrote recently, to cover the roots with a plastic bag or wrap with syran wrap to remove them from the base.
What I am going to do, is create a dwc system opposite the aerogarden... use the same pods just cut the holes in the buckets to match that in the aerogarden. I think this might provide less shock to the roots, as long as the water is of the same nature(ph, temp).
hope this helps
J