Using Flags to move Folders

Yes, you can use a flag to move several folders at once. Just keep in mind that if you add the flagged action to the process definition (in the Designer), it will only impact Folders that have not yet reached the Stage yet. If the Folders are already sitting at that Stage, they won't be impacted because no row has been added to the eWait table (which the Engine monitors for flagged and timed actions).