An alternative method (I just realised) is to define the docked cell for the Working Screen Environment only
Cell[StyleData["Notebook"]Cell[StyleData["Notebook", "Working"],DockedCells->{cells}]
Change the screen environment to Presentation, Slideshow, Condensed or Printout using Format->Screen Environment and then deploy / save as CDF via menu. This method however will keep the docked cell in the CDF if the Working environment is deployed to CDF.