Maybe this should be in Feature Requests but anyway here goes posting in the Z-Wave forum.
I just removed my Z-Stick and plugged in my new ZME_UZB1. I had one node (no.4) on the ZME_UZB1 that I had setup using Zensys Tools on Windows. I got a string of error messages saying devices no longer had a matching module in the controller. It also complained that node 4 didn't match the previous device type.
So I think Indigo should handle multiple Z-Wave controllers and the database ought to be able to differentiate between these different controllers so that Indigo realises that similarly numbered nodes on more than one controller isn't the same.
It would make transferring devices from one controller to another easier AFAICS
Maybe there is an easier solution that I have missed?