How does the folder comparison command Hide/reveal > Hide empty folders (View > Hide Empty Folders in the old-style interface) work?
This command isn’t a toggle command. When you use it, Merge will look through the comparison results list and hide any folders that don’t contain visible files. If you use the command before the folder comparison has completed, folders could be hidden even if they eventually contain visible files when the comparison finishes. Wait until the comparison has completed before using the command.