When you use DBCC CLONEDATABASE to clone a database that has query store functionality enabled in SQL Server 2016 Service Pack 1 (SP1), the runtime cache of the query store does not copy to the clone.
This fix is included in Cumulative Update 2 for SQL Server 2016 Service Pack 1.
Each new build for SQL Server 2016 contains all the hotfixes and all the security fixes that were included with the previous build. We recommend that you install the latest build for SQL Server 2016.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
Learn about the terminology that Microsoft uses to describe software updates.