I just upgraded to 5.1 for NCM and yet again my tools that I defined where blown away and I have to recreate them. I will ask this again...please get this fixed in the next release or something.
We really do feel your pain on this one. We added a new menu item ('Discover Devices') and our current toolbar control requires us to overwrite personalization for this to show up. Unfortunately, there is no merge option in the control. We spent an inordinate amount of time investigating how we would do merge, but short of replacing our entire toolbar control, this was not possible. Given all of our other priorities in NCM 5, we had no choice but to defer.
We'll look at this again for our next release. Until then, if you don't care about the ('Discover Devices') being available, you can manually backup the old toolbar (save old Configuration-Management.Toolbars file) and then overwrite new version.