I have never used the replace routine in the ISY. I find it better to delete the dead or removed device before actually removing it if it is still communicating and then adding the new one. Yes in a large system with a lot of programs it is a hassle. I also found rebooting before adding the new ones improved reliability if I used the same names for the device. Now I am changing the name just to be sure anyway. Dining was replaced with a new i3 so it is now Dining i3.
The next step is to run through all the programs and look for the green // areas where the device isn't found and replace them with the new device or updated scene.