Gotcha.
This is the first report of these specific files not migrating. Development is looking into it for beta 2.
Quit DEVONthink.
In the Finder, hold the Option key and choose Go > Library.
Go into the Application Support/DEVONthink 3 directory and copy the SmartGroups.plist and SmartRules.plist files into the DEVONthink directory in App Support.