The program having the issue is dbup3, which I didn't think ran when doing a refresh, but I could see why it might.
Maybe try running a database upgrade on both newdata and data. Utilities > Database Upgrade. Take the defaults and hit run. Then do it again, but change "NEWDATA" to "DATA" in both lines. Refresh.
If that doesn't work, post here and I will look some more. There was nothing overt that I found on a first glance through the documentation.