Any new operators you add to the duplicated layer in the Workspace will be local to that layer from that point on. If you want to control whether the mask is applied to both layers or not, use the schematic view to disconnect the mask operator from the duplicated layer. Then you can copy and paste it if you want a duplicate instead of an instance.
The schematic view is generally the best way to control this kind of behavior in combustion, since it shows the links in a way that the workspace can't. Use the workspace for general layer ordering stuff, the schematic for more complex operations.
-- Greg