When users create and edit queries in the Click Once version of the application, they have the option to select "Save as" from the File menu. This allows users to repeatedly make edits and save the changes as new queries within the open, original query.
However, this option is not available in the Web Shell version of the application. Users have the option to "Copy" the query before opening it for editing, but this doesn't allow them to rapidly make changes within the query and save them as they go. Users also have the option of re-naming the query in the "Set save options," but this overwrites the existing query rather than creating a new copy of it.
We are currently evaluating this issue and will update this article when we have more information.