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I'm guessing you had development data for the RM that didn't get updated -- more specifically, I guess you actually had development data there so when you did the CLI upgrade, it took that as the latest data and ignored the data in the XML files. That is really as expected in this instance, as the dev data is treated as being more recent, but that doesn't really apply if you mix and match the approach taken. In that case, the web upgrade will always use the XML data so it may be safer.